I've done it both in and out of the car. It's completely do-able in situ but you're going to have a ton of fun fighting with the tight quarters.
The MAF housing is bolted to the back of the intake with alignment pins and must be separated. Be gentle lifting the intake manifold. The after run pump wire harness is zip tied to the underside of the intake but must be disconnected first.
I highly recommend relocating the SJP to the firewall per Bigglezworth.
http://www.rs6.com/showthread.php/32...ugh-idle/page2
Personally, I've left the check valves alone. They've always been in good condition in my experience.
**The while you're in there list**
Replace the after-run pump. 078121601B is for an A6/S4/Passat (re-use the rubber insulator/isolator from the RS6) otherwise you'll probably only find 077121599A which is the pump and RS6 specific bracket $$$.
Replace the PCV check valve/boot; 034 has a nice set.
Replace IAT sensor. 078906161 (BOSCH 0280130060)
Good time to replace aging vacuum lines with silicone if you haven't already.
Clean the inside of the intake thoroughly; it's likely caked with oil residue.
Don't make the mistake I did and assume the intake manifold gaskets are shared across the belt 4.2 40V line. They are specific to the RS6 077129717R.
Replace injector o-rings.