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I'm aware of the other problems that are more likely to cause the transmission to jump out of gear. The transmission/shift tower is a rebuilt one from well known supplier. I was not real happy with it. Sealed main shaft bearings were used but the grease baffle on the front shaft was not used. Instead, looks like some sort of washer was used to maintain clearance. It doesn't shift to bad but was very stiff in the beginning. The flywheel housing using shims was aligned, less than .006 at all four points. My thinking on the clutch pedal clearance was that if there is a problem with the transmission/borderline jumping out of gear, then not enough pedal clearance would be the same as if I was riding the clutch. I will readjust for more clearance and if that doesn't fix the problem then I will try another transmission. If problem remains, then I guess I'm down to something else, possibly misaligned crank on the rebuilt engine. I have already tried a different shift tower. In one of Tom Wesenberg's post to someone else with same problem, he suggested putting transmission in gear and then keeping the tower aligned with cut off bolts and then lifting the tower off to inspect the gear mesh. I tried that but was unable to pry the tower loose. I'm just trying to exhaust all the possibilities before pulling the engine again.