Invoked the nuclear option. To answer all, yes exhaust fully off, yes used alfa centering tool to center clutch ; yes motor mounts loosened, same trans that cane off the car 2 weeks ago. Pilot bearing in great shape, not replaced.
Pulled the motor this morning and set it down. Got the clutch alignment tool and it went in , not easily, but not too hard either. Got a real input shaft and that was way harder to install all the way. So loosened the clutch plate, realigned , and torqued 18 ft lbs . Trans slipped right on, took 30 seconds. Reinstalled back into car.
Here’s what I think happened. When I pulled the trans off, I probably rested too much weight on the splines as I have no trans jack etc. the leverage moved the clutch plate on the flywheel and alignment was just a hair off. Enough to frustrate. I should have left the motor in the car and realigned it in-situ; alas done deal.
At 58 and a one man band it’s tough to do this stuff solo. Thanks to me friends who helped me out with support and wrasslin that motor back in. Now gotta our everything back together and see how we go!