Cool thread, very interested in seeing this develop. OP where in Boston are you?
As far as the swap I'd go with an S8 motor if you can find one, otherwise an S6 motor. I'd avoid the A6 4.2.
Since you'll most likely be using a manual its best to flash in a stock Euro S6 file. It is floating around (nefmoto I believe) and there are instructions on how to flash it (contact rednecktruck, he did his recently). That will get you running for free. If you are inclined a file like whats in my car at the moment will really liven the car up. I would forgo the VAST tune, the man who wrote that tune now writes for JHM and the JHM version is far more updated. My next revision should have SAI delete, cat delete, rear O2 delete and launch control, plus its significantly faster and sharper on throttle response.
The reason I say to go with the S6/S8 motors over the A6/A8 4.2 is mostly the cams and how the intake manifold works. The IM stages are operated via a vacuum solenoid that opens when the ECU tells it to, the issue is that the 3 and 2 stage IMs open at different times. Since the only factory manual tune is for the S6 its best to try and keep your setup as similar to that motor. Tuning off the automatic file is fruitless.
As far as driveline the A6 01e bolts onto the motor and only requires a bit of clearance around the starter iirc (redneck truck has a whole manual swap writeup in his signature for an A6 4.2, it will outline setting the driveline up). The 2.7TT flywheels and clutches work directly on the motor, mine has a VAST LWFW and Stg4 clutch.

Originally Posted by
biketsai
When you put it this way, why not ditch the B5 and go for a B6 S4?
The B6 S4 motors are a disaster in a lot of ways compared to the other V8s.
-Timing System: timing belt motors have the simplicity of a timing belt and standard accessories, which drops the cost of servicing both; the BHFs have chain driven accessories and a difficult to service timing system (some work can be done with the motor in the car, more indepth work requires the motor to come out)
-Rods: the S6/S8 motors have forged rods similar to the older 32v 4.2 motors, the A6/A8 4.2s have essentially the same rods as a 2.7TT, the FSI V8s have forged rods, the BHF has thin powdered metal rods with a tapered wrist pin (can handle ~450whp max)
-Pistons: iirc all the 40v 4.2s have cast pistons, the fsi motors have forged pistons
-Block Construction: The timing belt motors are lower silicon with chemically stripped bores, the timing chain motors have a higher silicon content and mechanically stripped bores. The issue is that the higher silicon content causes the block to expand slower, but since the piston metallurgy wasn't changed the pistons expand at the same rate and contact the cylinder walls (very small tolerances in the Alusil motors) causing the unfortunately typical cylinder wall scoring in the B6/B7 S4s
-Cams: The S8 cams have the same lobe design as the S4, the S6 apparently has an S8 intake and A6 exhaust cam, the A6 has both cams low lift. So if you have an S8 cam set theres no difference
-Intake Manifold: The S6/S8 intake manifold has the best multistage design for the V8 motors. The S4 IM drops a flap right in front of the TB and doesn't seal the long runners when it switches to the short runner. The A6/A8 manifold is a disaster, 3 stages and both flaps move right in front of the TB
-Exhaust manifold: The S6/S8/Early A6/A8 manifolds have a bigger outlet and 4 separate runners, the later A6/A8/S4 manifolds have a shared runner and smaller outlet
The biggest issue with the S4 motors is the cylinder wall scoring, and since most of the cars are gonna have some good miles on them you can't really take the necessary steps to ensure it doesn't happen (remove the precats, very diligent oil change intervals).
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