Depends on the ECU. Some can be coded to work in both 5pd and auto, some cannot.
IIRC the 2001 1.8t 6sp/auto files are completely different and cannot be cross-coded.
I could be wrong.
To be sure, i'd find a well defined 5sp file and start there.
Are you sure your file is stock?
If so, and 06A906032GH is correct, you're fine.
honestly im not sure if its stock. how would i tell? i just got my vag cable in today so ill be reading the file tonight. it pushes only about 8-9 lbs of boost tho and im pretty sure that's around stock(per the android torque app). So what your saying is it could be a different ECU then my stock one? Appreciate the help, i have a stock 5 speed one ill look at and see if its about the same.