Where do you live? From what I’ve heard most places in the states if you find a good shop should only charge around $1000. I only paid $900 and labor where I live is very expensive. Dealer is always gonna be the most $$$
As far as oem. Air filter, spark plugs, coils, all should be oem as far as our cars are concerned. Brake pads are an area where you could venture into the aftermarket. I know the popular one for our cars is the ebc redstuff, which will be my next brake pads when mine go. Most maintenance stuff should be kept oem that I can think of.
Other things might include aftermarket control arms, suspension, sway bar.
Oh and the water pump. The reason you replace them is largely due to the stock ones using plastic impellars and failing, whereas you can get metal ones. Its only a bit more money for the metal ones, no brainer there.