x2 on the "prick punching". No way is that an acceptable practice, and I'm surprised any machinist would even suggest that. Unless it's a perfectly smooth surface, it'll only dig into the thrust bearing and chew it up.
I never push in the clutch when starting, for the same reasons about lack of oil. But 'newer' stick shifts require you to do that. My '09 Mustang and my '05 Ranger have that "safety" built in, and I release the clutch as fast as possible so oil can get to the thrust.
Same thoughts on checking the input shaft to make sure it wasn't bottoming out. Sounds like you have good practices as far as not holding the clutch in and taxing the thrust bearing, so if something wasn't pushing the crank forward, I'm not sure what else could be the cause, other than a defective bearing or improperly machined thrust surface. Does the input shaft of the tranny pull forward? Because of the bevel in the gears, the shafts in the tranny naturally want to spread apart (fore and aft), so if the input shaft has room, it can walk forward, pushing it deeper into the crank. Just a thought.