It can be a little dangerous for the uninitiated to mess with that ball stud adjustment though? The problem is that as the clutch plate wears it gets thinner, so the resting position of the fingers on the pressure plate end up further out, reducing the throwout bearing clearance. If you were to adjust that ball stud up too tight you may have problems with the throwout riding the clutch years later (or premature throwout bearing failure)?
Ang, try to keep the driveline angles like they would have been from the factory, if you start messing with the height of the gearbox cross member you could find yourself with a bad tailshaft vibration?
Also, what was the clutch adjustment like before you pulled it apart? If the pedal would take-up just off the floor then maybe the clutch was simply out of adjustment, causing the difficulties getting into gear?
The other thing is it may not be the clutch at all? I recall we used to run auto trans fluid in M20/21's instead of gear oil as it made gear selection feel a lot better, especially when cold.