I have random cylinder misfires really bad when at idle and every stop I come to. Car shakes really bad. Then once I start moving it runs fine. Just had the engine out and rack replaced. What should I check? Its mostly cylinder 9 and 10 but not always. I also had the cats cut out and haven’t had a chance to get the jhm cables tune on.
Join the club I have the same but with all other 8 cilinders 
Pull the codes first and make sure there’s nothing else going on. After that you can swap some items around since most of your cylinders are fine. The problem is those two cylinders are buried somewhat.
Since the thing that changed is the engine was out, you should be looking at things that are disconnected in order for that to happen.
Were the injectors touched at all?
If not then the electrical connections to the injectors “should” be OK.
Though I do not know what they are, I am sure there are some measuring blocks you can use your VCDS to record and see what might be out of range and lead you in one direction or not.
Did a shop pull your engine? If so you may want to check with them as well.
Ed
I had issues awhile back with misfires on cylinder 8. In VCDS you can go into ECU 2 I think and there are blocks 15-19 will show you each cylinder in groups of 3 cylinders to show which cylinders are registering misfires.
For me it was cylinder 8. I could feel it misfiring at idle but cruising I couldn’t. Hard on the throttle I could feel it. After cleaning carbon again. swapping plugs around and even new plugs. New coils and swapping coils around I still had the misfire. Turns out of was the fuel injector. It just wasn’t working at some point while idling if at all. A year before I had replaced all the injectors with the JHM cleaned/flow matched injectors. Took me so long to diagnose an injector because I wasn’t believing that one of the JHM injectors died in less than 6 months (if it ever worked).
Check the misfire counter. I saw on mine that when cylinder 8 was not firing it was making that bank of cylinders run leaner and the computer was compensating by trying to add fuel to the entire bank.
I’ll look at those blocks. Its giving me codes for random cylinder misfire and its been jumping round. I have also got some fueling codes
P2189
P2097
P2195
P0159
When I bought my S6 it was shaking and misfiring at low rpm too.
For me it was the PCV system.
Try to remove the house for the PCV where the two houses connect and and seal the PCV off with your hand, leaving the breather hoses to freely breathe.
When I did this the shaking and misfiring was stopped immediately.
Unfortunately I can’t take a picture of how to do it, as I have removed the entire PCV system.
Ill try this in the morning. And yes I know what you’re talking about. This was a good suggestion. Thank you
I got around to changing plugs out today and I think that solved it. Drove for a couple hours with no issues. Idle rpms is good. No misfires on any cylinders at idle.