Definitely make sure you get a TDI trans to bolt up to that engine. Yes, a gasser trans will work, but you'll be turning much higher RPMs at highway speeds. I think my husband's TDI will sit around 3k or maybe even a bit less at 75mph. I've seen people putting in a gasser trans on their TDI and sitting more at 3500 or close to 4k at that point. Its worth it to use a TDI trans.
Mine: 20th AE GTI, BMP, 123k, stock...for now
His: '01 Jetta TDI, 122k, auto -> manual swap
The project: '84 Jetta GL TD, Giles IP, 2.5" downpipe and exhaust, full rebuild done winter 2010/2011