Well guys, we got the clutch fixed.
So here's the rundown:
The guide tube itself is attached to a set of needle bearings which the mainshaft rides on. So not /just/ the guide tube came loose, so did the needle bearing. Zero damage to the bearings, thankfully. However, up behind the guide tube is a sprung plate.
Link to diagram (can be seen as #12)
https://www.bullstuff.com/lamborghini-parts-manual/jalpa-1981-1988-jalpa-3-5-usa/17.24
On the Jalpa transmission, there is a plate BEHIND the guide tube that appears to be sprung to some degree, my guess is that it's part of a release when taking the actual transmission apart. I cannot find anything about it in any documentation or diagrams. However, it's held in place entirely BY the guide tube. What was happening was that as the clutch was being actuated, and from vibration, this tiny plate with tension was wiggling itself loose and pressing the guide tube further and further out, eventually causing it to entirely push UP against the center portion of the clutch. It was getting a mad amount of heat. We got that delicately ground down nice and smooth since it was a little shroomed out. No cracks, no major damage, all good.
Slathered her up with a good safe coating of white lithium, made sure there were nylon locking nuts on EVERYTHING, set the adjustment screw, got it re-aligned, double checked the plate, everything in place, and it's happy once again.
3 tiny nuts, one simple mistake, entire engine out. Learning opportunity. I'm glad I caught it early than late.
Car will be back in my garage tomorrow morning, and I will be putting it all back together and getting it back on the road. I've been working on a custom fusebox for the megasquirt.
One thing I DID find, which is odd, is that it appears the runners are starting to crack, at least 2 of them, on the edges. My friend suspected it could be due to uneven machining and vibration, and said usually on runners like that, they end up having braces, which mine have none. I'm going to take the runners off (easy to do with the engine in the car, very accessible), and braze the aluminum and see if I can easily repair them. I think I'll just go with a thicker gasket on them. It's also possible my old machinist torqued those buggers down wayyyyyy too tight.
I want to address it before I go driving, in the off chance it's going lean on one cylinder, the last thing I want to do is end up melting a nice new shiny set of forged pistons.
Feels fantastic to have that out of the way. I am, fingers crossed, going to make it to the festival of cars this year.