You got a lot going on. Lol.
When the engine was last "rebuilt", bucket size wouldn't change unless the car got a valve job. If they did grind the valves and not the top of the stem. That would definitely close up your cam-to-bucket clearance and cause issues. But that's one of many places the wind could go.
I know you have a built bottom end, but that doesn't make it immune to other typical mechanical failures like broken rings, etc. Also if your engine was built with soft pistons (the ones that handle 1000hp, forgive me for not having the alloy number off hand), those pistons do wear out rather quickly and can lose compression if you're expecting to daily drive them.
As far as the clutch and staying engaged, a friction disk failure can cause this (pieces coming apart and getting lodged between the friction disk and pressure plate/flywheel) or a hydraulic failure, whether that's master or slave.
Either way the course of action here should have been an entire teardown, but it sounds like you only removed the head with the engine in the car, right?