if you were to use the MK3 trans on the MK1 caddy, you could just swap the flanges from the MK1 tranny over to the MK3. the MK3 flanges stick out about a half inch more, and so custom shafts or mk2 100mm ones will be required.
i've done it, and its not too difficult. you just need new seals (its REALLY hard to take them out without damaging them) and a C clamp as it will be spring loaded (one side will go on easy, and the other will be pushing the spring, so you need the c-clamp)