I just want to finish up this thread, since the problem has been resolved.

Lessons learnt:
- Do not use an Audi a3 ecu in a VW mk4 golf gti.. The ecu will work, car runs fine, but minor features missing.
- The Mk4 Golf GTI and the A3 1.8T engines are NOT identical, they look the same but they are slightly different. For example, the throttle body are different and will prevent a golf from doing a TBA with an audi ecu. In saying that, the cars throttle body will self adapt over time.
- NOT all ecu's have the ability to run cruise control, the AQ ecu in the audi line up does not have the extra hardware for cruise control. (confirmed with ETKA).

Thanks for everyones help, and big thanks to Gavin for helping me out.