The biggest difference is that the A3 the engine runs across the engine bay (transverse) so the drive has to be turned through 90degrees into the gearbox. The A4 has a longitudinal engine ie the block is in line with the gearbox. On that basis, I'd guess the engine mounts and drive would be trickier to connect up.
Best looking for something from a sister car to the A3 i.e. Golf Mk4, Vento, Leon, Toledo, TT, Octavia