I'm finishing (very slowly) the same project
Motor and trans from a '92 eco-diesel.
The 2.0 serp bracket doesn't fit. I got one from a 1.9TD but used the AC and alternator from the 2.0 gas motor.
You also need the harmonic balancer from the 1.9TD
Emissions: no idea, I'd guess they're the same as a 1.9TD and I'm hoping that will fly with inspection.
Motor mounts & Trans: To simplify and save money, I moved the whole subframe with brakes, A-arms, motor mounts and all from the mk2 to the mk3
My mk3 was automatic so I used the mk2 5 spd. I would have loved to use the mk3 axles but being an auto, they don't bolt up to a 5spd.
To make it more fun, The mk2 axles are shorter than the mk3, so it was easier and cheaper (for me) to swap in the whole mess.
The upside is I didn't have to buy new axles, didn't have to convert from 90mm to 100mm flanges on the trans, the downside is I have solid front rotors

until I can afford different
mk2 mk3 steering racks have different splines. I used the mk3 one with the mk2 tie rods.
Speedo: haven't hooked it up to the mk2 trans, no idea how, as the mk3 was electronic and the mk2 has a cable, anyone want to make a suggestion?
Thats all I can remember for now.