if you want a 2.0 litre 16v engine, use the whole thing from a mk3, and it is apparently a very straight forward conversion with no loom making needed (i think you just plug the new wiring into the existing fuse box).
Similarly simple is using a 2.0 litre 8v bottom end only from a mk3, with the other mk2 head and bits bolted on.
These volkswagen engines are generally very reliable for very high milage's, so you may want to consider getting the whole car first, cleaning it up and playing with it as you like, before spending money, slightly unnecessarily, on the engine. It would also give you the chance to consider one of the simple engine conversions once you have seen how a standard 8v drives. As doing it your way means you have committed yourself to the 8v engine by spending lots of money on it..... It's just an unusual way to go about it ( tho I can see the sense if you want to rebuild an engine without the rest of the car in the drive).