Ok so i had the stupid idea of rebuilding my gearbox myself, everything seemed fine till i reached the point where i put the main part of the case bk on, then a notchy feeling appeared when turning the shafts by hand.
When i put it bk in the car it made a terrible whiny noise which im pretty sure is this notchy feeling magnified, 3 times ive had it out and stripped it but can seem to find the prob.

P.S reason i rebuilt the box was the mainshaft was knackered.

 

Take a different mk4 box and take ur sper diff into that one? Maybe easier then finding the problem?