Hi, if you are fitting an STi box then the rear diff will require to be changed, this is definate. UK cars use 3.54 rear diffs, Jap cars use various (3.9,4.11,4.44), but none of them are 3.54.
Arch you are not quite right about the rear shafts, the R160 shafts/rear diffs changed in '99. So a pre 99 diff of the correct ratio will be required to use the existing shafts.
If the car is a UK car we don't need the gearbox codes it will be TY752VNxAA (x being variable depending on model year) UK cars retain same gear ratios and final drive ratios across the model years.
The code from the STi box is essential though to determine suitability. BTW, if the rear diff is wrong, it won't be the rear diff you will kill, it'll be the centre.
So in summary, get the finger oot and tell us the box code