Hope I didn't come across as too rude.
You will want to use the transmission from the TDI. That will also require swapping over the cable shift setup, and the hydraulic clutch.
Not only are the ratios of the 020 style transmission that comes in the cabrio incompatible, but they are an already fragile 'box that can barely handle a tuned 2.0...That is why heavier (B4 passat 2.0's) and more powerful/torquey TDI's came with 02A style transmissions..they are quite a bit more beefy..well worth the effort.
If you really want to do it right the first time, find an 02J style trans from a mk4 TDI. They are even better than the 02A.
If money has no limit..find an 02M from a european TDI..6spd would be nice..