Finally, an update. I towed it to the transmission shop on 11/20. Today (11/29) they put it up in the air and started investigating. They called at first because they were able to hold one wheel and turn the other, and that doesn't make sense to them as an LSD. Basically it makes you think the differential is internally broken since an LSD should well, make the other wheel turn as well eventually. I figured well, it must be broken. UMS said it was funky and the trans shop says the held wheel doesn't turn. I called up the local parts yard that has a 97k mile transmission and ordered it, figuring I'd just have to swap the trans with a stock one for now, but then...
I decided to call Quaife and ask them how I could know whether there's a failure in the differential. They emailed me me a differential checklist. Turns out it's supposed to do that. The shop said the trans fluid was low as when they removed the easy passenger side axle, nothing came out which is unusual if it was filled to the 2.6 qt recommendation. If it was under-filled (to the original factory specification) that would cause the excessive gear noise I was hearing during coasting and such.
I figured well, maybe it was just the CV joints that caused the clunk. Told them to just replace the driver side axle that was stuck, fill it to 2.6 qt and let's see how it works. On their test drive, they think the clunk is just something torquing under load with the engine/trans movement and hitting something, like the charge pipes touching something. I don't think so - I am pretty in tune with my car. So I'll have to look and try to find another source of the clunk. They weren't able/willing to replace the driver axle since it was stuck in the diff, suggested I just drive it for now.
As far as the hydraulic issue with the pedal stopping halfway, apparently it works perfectly fine at the moment. I had Clutch Masters create another billet throw out bearing (number 2 of 2 in existence) and I bought a spare clutch master cylinder and hose setup in order to evaluate how to improve it. I immediately see the "dry-break" plastic stuff UMS was talking about, and can see how that could cause an issue. My plan is to cut and flare the hard line from the master cylinder, and connect a flexible braided hose to the Clutch Masters throw out bearing. I
think the Clutch Masters setup is a 2-hose design, which would allow you to make one hose end a bleeder, making it super simple to ensure the whole system is bled. I think that will prevent any weird air-lock occurring in the original plastic configuration.
