Re the clutch pedal hitting the frame. My 40 frame had a sort of recess where the x-member leg meets the frame. this allows a little more travel before the pedal bottoms out. I don't know if the 39 had this, or if the 35 frame has it, but if the pedal is hitting the frame, that might be what is causing it.
Edit: I just saw you ran it and it is fine. that's good. Did you do anything to the clutch pedal? Or was there sufficient travel as it was?
Mart.