Although I have not installed a 1.9 TD into a mk2 I have removed one and I also installed a 1.6TD into a mk3.
Motor mounts : you need the mk2 ones, the mk3 ones are different. The bolt right up to the block though
tranny: Any 8v tranny bolts up to any 8v engine, gas, diesel it's all the same. The mk3 tranny is ALOT taller then the one in the mk2 so I'd considier swapping it in. If you do, mk3s have 100mm hubs on the tranny, mk2s usually have 90mm.
Pump: The mk3 pump has 3 wiring connections IIRC, mk2s only have 1. Not sure how to get around this, you probably just need power to the stop solenoid to make it run
coolant sensors: mk2 and mk3 are different but all you need to do is swap the coolant flanges from the mk2 onto the mk3.
Exhaust: you'll need the mk2 DP setup (the one bolted to the turbo) or customize the rest of your exhaust to go with the mk3 DP
Alternators: slightly different wire connections, all you need is a soldering gun
Starter: Use the mk2 starter
I think that's it