Im planning to transplant a Gen3 turbo engine into a Gen2 turbo engine bay, including the Gen3 engine harness. I have never had a Gen3 engine before, I know the primary differences between the generations but when it comes to fitting in the engine bay Im not so sure. Are all the ancillaries pretty much the same? Is this pretty much a straight swap? I would rather know the potential obstacles before I get the transplant underway.

When i did mine it was only minor wiring changes that had to take place. Reuse the cable speedo drive if your car is cable currently.

ok thanks Trav

I did this swap last year.  Physical fit is the same.  I believe the exhaust location at the end of the dump pipe differs by a few cms (swapped exhausts so can not confirm, but it is what everyone says).
 
Swap over the engine loom, then you will need to do some minor repinning in the fusebox, the ecu and the boot plug.
 
As above, reuse your gear drive speedo sensor.
 
Air con electrical connection is different if you are keeping your old AC hooked up to the lines.
 
Also if history is unknown, consider doing the timing belt, water pump etc while the motor is out and it is easy.
 
Cheers

Forgot, the charcoal canister is different, as is the engine bay fan controller in the boot, the FPR socket.  If you have all he bits off the gen3 half cut just swap all the bits over.
 
Cheers