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Update:
Primary is back in one piece. Just need to adjust the clutch, add fluids, put floorboards back on, set the shift levers, etc. Hoping to get a test ride in this weekend sometime, thanks to the holiday. Today was a good day.
Absolutely stoked! Maiden voyage test run is in the books. She is mechanically back in one piece. Transmission shifts smooth, clutch feels good.
Only issue was on first fire up she puked engine oil out the breather at me. Imagine my horror thinking a bad seal install or something. Pleasantly surprised to find it was just engine oil that seeped while it sat idle for such an extended period of time.
Only other non-issue is the neutral light also comes in in 5th gear. BUT it finds neutral easily, even when running. So that issue is solved as well. Happy man here!
Oh and after much thought, I have come to the determination that the ultimate problem was simply a failed 30+ yr old drive belt. As soon as the first set of belt teeth came off, things just snow balled from there. The grinding sound, I believe, was the drive sprocket searching for belt teeth. Then the slipping and grabbing was the same thing. When drive sprocket would find some belt teeth the force would then strip off more teeth.
That being said I could have saved myself a bunch of time and money by just replacing the belt. That would have only cost about $300 in parts. But knowing I also had a few other shifting nuances I dig deeper. Very happy to know now that the trans and primary bearings are all new, shifter pawl is new, and the gear set has less than 15k mi on em. I would say that's pretty good for a $1200-ish investment in parts and tools. No idea how many labor hours I have into in it. Doesn't matter, it was worth it.
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