Thanks guys. The idea of this thread is to be the standard for new and used owners to get a good look at all the issues and bugs that can come up from owning one of these great cars.
I’ve read lots of built threads, collectively all of them cover the known issues. However none of them singly has all the issues. Let me tell you this car has just about every issues you’re going to see. If I don’t see it I’ll make sure to talk about and or post about it.
With the front of the motor sorted out with a new tensioner unit from JHM along with a needed snub mount and the removal of the Aux rad and the back of the motor sorted out with the replacement of the timing chain parts from JHM and the upgraded clutch, it is time to move on to the top part of the motor and some of the more performance driven parts.
The three major foundation performance mods you can do for the 4.2 S4 are. Exhaust, tune and intake manifold in that order. The 4.2 S4 makes great power stock but the stock Dp’s and exhaust system choke off the power. Doing a performance exhaust will free up the flow needed and adding the JHM tune will allow the ECU to let the added power make its way to the pavement. With those two staple mods you’re going to still be faced with a little shortness of breath up in the higher RPM’s.
There is a two-part solution to the shortness of breath in the upper RPM range of the S4.
One - Add an aftermarket air filter. The biggest mistake some people have made is adding an open element filter and doing away with the stock air box. This is a terrible idea. The stock air box on the 4.2 S4 is a great unit and actually works in a semi ram air fashion. The air box becomes pressurized and is a high-pressure zone. This high pressure air box zone allows the rapid flow to the low-pressure zone (the motor)
Right now one of the best air filters is the K&N. The only downside is the K&N units don’t fit all that well
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Keep that in mind and just make sure to put a little extra time installing them. It would be nice to have a stronger option that fits better but, for now, it’s a great proven option.
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The reason you want that extra flow from the air filter is to feed the JHM intake manifold. For those of you who have this, you can feel the extra hp and flow in the upper RPM range. It makes the entire RPM band move by swiftly and keeps good positive power through the entire RPM range.
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Since I was swapping out the old intake manifold for the new one, I took the time to swap the injector seals. You need to pull the injectors out of the old intake manifold anyways. While you’re at it, it’s a great time to replace the seals.
As long as you have a steady hand and some patience, it’s a good maintenance move
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After the last details got sorted out with the intake its time to move on to some of the last parts before looking to put the motor back in the car.
More maintenance things like
Motor mounts
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Always good to look into stuff like motor mounts, starter, and AC unit. It’s much easier to install these parts with the motor out of the car. I opted to pass on the starter unit as I knew my AC unit was probably bad. The AC units on these cars fail very easy.
As I was getting ready to start getting the wire harness back in place I noticed an unsmooth feeling just under the wire cover.
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This is the wire harness that goes to the secondary air injection pump. I had noticed the car had a secondary air injection code originally but on inspection, everything looked ok.
I figured just for inspection sake I’d look at the wires.
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Not in good shape. Here is a closer look
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The coating on the wires had actually become brittle and broken off the wire. After talking to a few people, it turns out this more common than I knew. If you see someone with a mystery secondary injection code and everything else looks fine. This is a great place to look.
Wow! that is wild, I have never seen a wire come apart like that.
This thread is excellent, thanks for taking the time to detail all of this.
Great write up. Love the updates
Great thread! Thank you
Where did you put that washer in the first pic? I was wondering when I did this myself… I don’t see it in your “final pic” like I do in mine.
As for the washer. It’s actually an extra washer that you use to space the roller if needed. Most of the time it’s not needed it’s just a bonus part. It’s best to just put it where you put yours. It’s a good extra washer to use ontop of the bigger one just for the sake of using it.
After the repair on the wire harness for the secondary air. I just decided to remove all the secondary air components to save the hassle of any issues down the line. Secondary air is an emissions component and since I’ll be removing my Precats it wouldn’t be doing much good anyways.
After I removed the secondary air system. I figured I’d check out the wire harness to see if there were any more surprises. Turned out there was.
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In this section of the wire harness is the fuse for the secondary air. The fuse is very big. Turns out it was blown.
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It’s a good thing that fuse blew. With how big the wires are and how much current it would take to blow the fuse. That kind of thing could have started a fire. Seeing this prompted me to take the search through the wire harness a little more in-depth.
The rest of the harness actually looked good. I stumbled across a broken clip on one of the rear 02 sensors. I couldn’t get the plug to stay in. The plug is a friction fit with a clip. When the clip breaks you’re just depending on the friction. Knowing that if the 02 wires short out it can kill the ECU I decided it needed to be more then just pushed in
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Zip ties work for a lot but I tend to think they look cheap on stuff like this. I didn’t have much of a choice so I went with it.
Another big issue with clips is something EVERYONE probably has an issue with and that’s the coil packs. I don’t know of too many 4.2 S4’s that I have seen that have all their coil pack clips in perfect condition. On most cars, at least, one of the clips, if not more are damaged.
Since I wasn’t excited about the idea of zip tieing my coil packs connections on. I bought a used wire harness and decided to do the repair.
I know this can be intimidating so I figured I’d show how I did it if that might help some people. Not sure if this is good enough for a DIY but it should take the mystery out of the fix.
I’ll show it off the car to make it a little easier to understand.
The idea here is to take the wires out of the bad clip on the left and transfer them into a new or better clip as shown on the right. You can see the standard broken tab on the clip on the left.
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To swap over the wires you need to go through a few steps and to understand what everything looks like.
To start the plug in my hand has two active pins in it. They are the silver part just above where I’m pointing to. If you look on the table you will see a clip with one of the pins removed. This is to show what it looks like in each state.
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To get the pins out. You need to pull out the lock bar. To identify the lock bar just look on the side of the clip. You will see it through the window. On this clip and for the coil packs it is a kind of off-pink color.
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Here is a little better angle
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Here is the top view.
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The next step is pretty easy. Get a pick or something very thin. simply put a pick down onto the lock tab and start to slide it out towards the open hole.
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Here it is further pulled out.
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and another angle.
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This is what it looks like with the lock bar out. You can see it laying on the table.
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Now that you’ve gotten the lock bar out. You need to pull the wire pins out. The wires most times won’t just pull out. What you’re going to have to do is to compress them together and pull them down. Getting something on each side of the pin like this paper clip works great.
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From there you pull the pin out
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After you have the pin out you can relocate it into the new connector.
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A few helpful tips.
One, the pictures above I used are for example only. One of the connectors would normally be connected to the cars wire harness that is on the car.
Before you remove any of the wires and put them into the new connector. TAKE A PICTURE OF THE OLD CONNECTOR WITH THE WIRES IN FIRST. One quick way to ruin your day is by putting the wrong wire in the wrong location. It’s a quick way to cause major issues one of them can be wiping out your ECU.
On the connector face, you will see numbers. You want to obviously make sure the same number wire gets into the same number or the same location on the new connector.
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Happy to see a full build thread! Will have to keep coming back for updates! Two thumbs up emoji
Hey good to see you made it over. Thanks, you should know about big projects. You’ve navigated several already. Do come back and check in. I have lots more updates and some fun exciting surprises at the end of this project.
After getting the wire harness, all sorted out. I made sure to get the wire harness cover so the entire project would look like new. After the time, I spend on the coil pack clips having a broken wire loom cover didn’t look right.
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The exciting part is getting closer and closer. I’m now about ready to start putting the rest of the parts back in and get this motor back in the car.
The next big decision came up. What to do about the exhaust? In this case, the down pipes. The car already had a great sounding fast intentions cat back, but what about the down pipes? I didn’t even pay much attention to see if the down pipes were modified when I was taking the car apart. One of the best things you can do for these motors is to remove the Pre-cats. The removal of Pre-cats is good for both performance and the long-term health of the motor.
With that in mind, I grabbed the down pipes and took a look. For those of you who don’t know what a Pre-cat is or what this all looks like. Here you go.
This top canister is what hold the Pre-cat, a large cat very close to the manifolds. This is only here for start up in cold weather. So, in reality, it’s only on the and in place to act in emissions support. It causes more harm than good, considering just about everyone can pass emissions without these. The actual intended use is for the first 2 min of the cold start up. After that and for the other 99% of your driving it’s just allowing heat to back up into the motor. The Pre-cats have been linked to part issues in warpage of the blocks.
Here is what it looks like from the outside
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Here is a peak on the inside
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The honeycomb cat is there to trap exhaust gas. It’s a restriction and it kills power.
The removal is messy and dirty. The material inside can emit quite a bit of unhealthy dust when trying to break it down. For most it might be good to look for someone else to do this or look for a set already modified. I believe JHM has an exchange program.
I made a DIY video if anyone is interested. It’s messy but possible to do at home. Here is what it looks like when you start breaking apart the cat material
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Once removed this is what it looks like. I didn’t have an after picture so this is from someone else.
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The material you remove from the inside looks like this. Here is a small chunk
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With the Pre-cats removed and the transmission bolted up. I was ready to bolt the downpipes back on the motor.
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If you remember earlier in the teardown and removal of the motor my slave cylinder basically disintegrated once I removed it. As you can see I installed a new much-needed unit.
After the install of the slave cylinder, I was excited about getting to the end of my big box of JHM B6 S4 rebuild refresh parts. Just as I was getting ready to start lining up the motor to put it back in its place. I noticed a few more parts I had left in the box from JHM. It was a hose and a barbed fitting with some clamps. It said, repair for return power steering line. I know this is a common failure but my first inspection of the line looked ok. It’s a good thing JHM sent that line a closer inspection showed the turn hose wasn’t in such great shape.
First glance the hose looks ok. Look at the bottom hose. It has signs of it failing but you might only see it if you look closer.
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Can you start to see it now? It’s the bottom hose. You can see witness stretch patterns in the outer cover from the hose swelling.
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Here is a better look. You can clearly see the stretching of the hose cover material. This hose was swelling already.
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This can happen when your wife drives the car and she turns the wheel all the way to one side to the point the steering locks and she holds it there while she tries to back up or turn sharp. This can happen under other harsh driving conditions but for the most part, I said wife, because us guys know not to turn the steering wheel all the way to the lock position and hold it there while the car is running. 
This hose was going to let loose very soon. It’s great to replace it now while the motor is out. It’s much harder when the motor is in.
The replacement was simple. I followed the hose back far enough where there were absolutely no signs of hose swelling. I made a cut in the old hose and put in the new hose connecting the two with the provided barbed fitting and new hose.
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Here is the install after. It’s the bottom line. It’s a simple quick fix that’s well worth the time and money. This is one of those real pain in the backside things to replace. It’s easy to overlook it, but project from the grave didn’t fail us here. Yet another part that is prone to fail comes through.
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Love reading the updates, virtually to a T what I am doing to my car lol. Keep the updates coming.
Exactly this is shaping up to be everything I have already done. This is trully a thread each new B6 and B7 S4 owner should read. It is a great road map for everyone to see
After the new power steering fix and all the wire work. I was ready to go. I had the transmission all bolted up, the slave installed and the downpipes done and ready for the motor to be reinstalled. Before I stuffed the motor back in I thought about how much work I had done and that It would be a good idea to clean up the front of the motor and install some new valve cover gaskets while I was at it.
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The valve cover gaskets are much easier to do while the motor is out of the car anyways and I wanted the motor to be clean on the front side so I could see if there anything leaking. One tip for installing valve cover gaskets to help them last. Put a light bead of silicone along the bottom and corners. Oil will gather in that area and its good to help seal it with a nice bond you get from silicone.
AT LAST, THE MOTOR GOES BACK IN.
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Getting everything to fit in its place nicely
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With the motor all set in and the wire harness plugged in, it was time to next put the front core support on and to start adding fluids. Justincredible wrote a good article about this. I’ll try to find it, and link to it. One of the concerns people have is what coolant to run? Before I add my thoughts, let me say. If you ever question what parts or fluids etc to add, always use the OEM suggested or listed fluids, parts listed in your service manual or otherwise noted on your parts.
The quick version. Audi has a formula that removed certain chemicals from what was the standard coolant used in domestics. Audi had a formula for the older VW’s (G11) where they created a new chemical mix. After G11, G12 was created, for the new G12 Certain chemicals from G11 were removed and or changed. For most cars from 2000-2010 G12 was the recommended coolant. When it came time to create the new G13. VW took some of the additives removed from the G11 coolant to make the G12 coolant and added back in some of those chemicals for the G13 formula. It all is compatible forward. So you can use G13 in G12 cars but not G12 in G13 cars. So when you look at the additives allowed the DEX-Cool has a very good mix. I found and have used over the years, anything that has DEX-COOL compatibility. When you break down the chemical chart it’s very close if not a match for the standard G12.
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After you have topped off the coolant, checked the oil, and made sure to top off stuff like power steering
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It’s time to prime the motor. When you prime the motor, this gives the oil and other fluids a chance to move around and the oil pressure to get pumped up by using low RPM low friction. When you start the motor even though the RPM is under 1000rpm this is still a harsh environment for a motor and supporting systems that haven’t been primed up yet. The power steering pump doesn’t like to be started and ran without being primed
and now that you did your timing components they need to get oil up and into the adjusters and lifters before you start the car. When you prime the car its also a great time to check and see if you have any other electronic connections you might have missed or small hoses you didn’t connect.
Here is how I prime the car after a long down time.
Go to the fuse box and pull off the cover. Located the fuse for Engine management on the list and its spot in the fuse panel… This turns off the injectors and fuel allowing the starter to run without any chance of the motor starting up. So you will be able to control the motor from the starter.
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Remove the fuse
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Key the car up and wait to see what lights come on the dash. Check any of the error lights and correct as needed.
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After you have checked all your connections and hoses you can turn over the car with the starter. Since you removed the fuse for engine management the motor won’t start but it will turn over with the starter. The low motor speeds provided by the starter are perfect for bleeding the system. The things you’re bleeding are the oil, the power steering and filling the AC. Keep in mind your AC compressor unit probably already failed as they are very brittle on these cars. So, consider replacing the AC compressor unit before getting to this stage.
After a few minutes of priming the system checking all the fluids, you can put back in the engine management fuse and get ready for that first start since pulling the motor out. A few last things you check before you officially start the car. Pull up your vag com and check for any codes. Clear all the codes and keep your vac com up and running for the first start. If you’re still nervous about all your work and want to check one more time on the health of the car before you start it over. You can go into vag com and in the engine section do an output test. This will go and check out and test electronic parts like the injectors, throttle body and electronic adjusters on the motor. From there you can proceed as needed depending on your results.
For me after I primed the motor I took a deep breath and fired the car up. Upon the first start expect to hear some clicking and ticking as any of the lifters that didn’t get enough oil start to get that oil now. Also, make sure to keep an eye on the power steering and the coolant. Now on the first start expect to see the coolant drop as the motor takes it in. I usually let the motor run for a small bit then I shut off the car and check over everything visually and on vag com. After my start I had no issues so I cleared everything out of the way and was getting ready for the first test drive in a long time.
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.The dredded starter fail
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Sure enough, the one part that WILL fail on the car failed. After 8 or 9 prime sessions and 2 complete starts of the car the starter gave out. Just to make sure I pulled down the starter and tested it.
So, the first test drive would have to hold off yet another day until I could look further into this. The project continues…
Glad to see so many getting something out of this. If you have any questions, feel free to post them. If you feel I missed something, feel free to ask. I do want this to be a very through step by step of what everyone will see at this point when working on these great cars.
this is fantastic! thank you for sharing
Just gotta say, you’re da man CV. Thanks again for all you do. Your work is what made me love my S4!
LMAO if its not one thing its another. Oh well, starter replacment shouldnt be too bad.
It never ends with this car, right?
Great updates as always. Can’t wait for the next installment.