New shafts arrived today - top notch. Well impressed. No splits at all in the boots.
For anyone interested - the shafts from a TT Quattro will indeed for an S3 with no problems at all.
So..... The inner CV joint that was knocking? Oooooooohh dear. It was FUBAR in a whole new way.
For openers, I removed the CV from the box and found the circlip for the joint sat in the back case, in the grease. Not good.
Anyway, the damage was quite impressive to be fair. The balls were OK-ish - a few dents and grooves aside.
The bearing race and inner cage however, were impressively broken.
Even the circlip has signs of wear on it.... Somehow.
Anyway, I have my suspicions that this may be the cause of the my mysterious 'clunk'.
The outer boot also had 4 separate tears in it, and was dry as a bone.
PAS not fixed yet so couldn't test drive