The fork for the throw out bearing is in the top cover, pivots on 2 half shafts, one of which is hooked thru linkage to the clutch pedal- is this correct? If so,is the fork positioned correctly? There should be a set screw that's screwed into the fork that indexes the fork to the shaft, does this sound correct & is it indexed correctly?

If these check out ok, I'd measure how far the fork moves forward when hooked to the clutch pedal, then make up a test rig & move the throw out bearing the same distance with the top half of the cover removed & check the clearances that way