All 01A transmissions are interchangeable. Just the gearing is different on the 2.8 versus the 1.8t (don't know engine codes). The B6 A4 uses the same tranny (5-speed, not the 6-speed), so you can use one from there. Simplest and cheapest thing to do is just find a used tranny and swap it in. Also, choose a clutch for your future goals so you don't need to replace it again later on. And when it comes to the engine, it is the same damn 1.8T engine found in all VAG cars, with slight differences between engine codes. Since you come from the Vag world, I am pretty sure you know what these cars are capable of. I'm at 145k and just installed my T3 GT2871R like 2 months ago. Internal upgrades coming along later with fresh hone/piston rings. Are these cars worth dumping money into? That is something you need to answer yourself.
Here is info on the engine codes of the B5 A4 and how they differ (1.8t content):
97-99.5 is the AEB engine with an 058 short block. You should already know about the AEB cylinder head, so not going into that. It is a drive by cable throttle system and has a narrow band primary o2 sensor. Stronger rods than the 06A block because of the larger wristpin (20mm vs 19mm). You have no SAI, no MAP sensor, and you have an ICM for your ignition coils. All the specs of an 058 block apply. This is the pre-face lift (minus 99.5) as far as the body goes when it comes to the B5 A4.
00 is the ATW engine with an 058 short block. People call this the bastard child because it is DBW throttle system, still has the o58 block, and the primary o2 sensor is still a narrow band. Other than it being DBW, same thing as above. Basically a DBW 058 block with smaller cylinder head found on the later model A4s (00+ is when they made the smaller port units). As for body goes, this is the facelift version of the B5 A4.
01-01.5 is the AWM engine with 06A block. Has all that emission crap, including SAI. Has small port cylinder head, is a DBW throttle system, has MAP sensor, has wideband primary o2 sensor, no ICM (4 wire coils with ICM built into them), came with slightly larger injectors from the factory, came with more HP (more boost) from the factory, has vented valve cover, and all the stuff that comes along with an 06A block. This is the facelift version of the B5 A4.
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