Mate, with regards the vr6 conversion... Do yourself a favour, buy a vr6! I had the same plan to drop the vr6 lump into my mk3 gti, but to be honest your just better off buying a vr6, less hassle and no bloody nuckles! I managed to find myself a beautiful black 4 door vr6 with 90 000 on the clock all for £800, an absolute bargin in my opinion!
If a vr6 is what you want... Then buy one! Trust me you will not be sorry!!!
just takes time to find the bargins!
Happy hunting!