A couple readers suspect that the pilot bushing was dragging on the input shaft splines. One said that it was due to not having the dust shield between the engine and transmission which would have spaced them apart a bit more… but this engine doesn’t have a dust shield, at least none that I’ve ever seen. After a bunch of measuring with a straight edge and calipers, the pilot bushing had 0.015″ clearance to the spline shoulder, so there shouldn’t have been any binding, but it was tapped in a bit more. I’ll also double-check that the input shaft shoulder can’t contact the crank directly.
Sending in the clutch wasn’t a complete waste since it’ll rule out one possible cause. They’re also going to swap out the diaphragm for a lighter part to reduce clutch pedal effort, as long as I can deal with it “only” holding 500 ft-lbs… that’ll do! They’re also updating the clutch assembly to the latest version; while I’m not sure what that means exactly it seems like a good idea. Of course after this is all over – and assuming the problem goes away – I’ll never know for sure what root cause was since a handful of things were changed at the same time.