You've got to use the ratios (1st-5th) specified in the ITCS. That means (for a vast majority of MkIII Golfs) either a CHE or DFQ code 020 transmission. There's an alternate ratio set that's allowed, that documentation says came in a few Golfs but they are HARD to find as a unit.
You can use a different final drive gear set (e.g., the 4.25 from a MkII diesel) but you have to do some clever parts mixing to make that work and retain the correct gear ratios. You cannot simply use a different 'box (like from a MkI GTI or MkII Golf) because the ratios will be wrong.
Do yourself a favor and get in touch with Cameron at Conover Motor Sports. He knows all of the technical details.
Kirk