yeah i did this to J_S' car, was a straightforward swap but wasn't as easy as the 2.0 bottom end I fitted to my 8v!
The loom will plug in IF you have a 90 spec car, but it isn't quite as simple as that, there are 1 or 2 wires that need swapping/splicing between the MK2 & MK3 engine loom.
You also have to spend a while binning all the crap from the MK3 loom that you dont need, lighting etc etc. Best way is to pull the old MK2 loom out, keep the lighting part then work on the MK3 loom stripping it down, then compare what few plugs you have left to the MK2 looms, swapping/splicing wires where needed.
Best way to strip the MK3 loom is to start with the ECU loom, and bin EVERYTHING that isnt connected to it, if it aint running to/from the ECU ore one of the engine sensors you dont need it! Main one to watch out for is the lambda probe plug, it has 1 wire to the ecu and earth/power wires to the fusebox you'll need to keep, and MAKE sure you get the diagnostics plug, and if its a post 96 get the key from the car along with the transponder ring from ignition surround, along with the control box and associated wiring.
Once you identify unneded wires, use my fusebox FAQ to treack down all the pins on the MK3 plugs, to double, double check you dont need them, then chopy chopy.
After that the hard part is over, engine will bolt straight in using MK2 mounts and mount brackets, keep your old gearbox unless it knackered or you plan to go for BIG power, and use a std MK2 16v manifold & downpipe for an easy life. The OEM VW units are proven to flow very well
