Not Ranked
I have an aluminum 351W based 427 hooked to a TKO600. The clutch is a Mcleod RST. The bell housing is a QuickTime. When putting things together I checked the runout between the bell housing's tranny opening and flywheel. It was out of spec (~.015"). I had to pull the block alignment pins and replace them with offset pins. Got it dialed in to ~0.003 TIR (total runout). I had trouble getting the slave set up - took it to Eric Voss to do it right. The lines are all run as delivered from Hillbank. No heating issues. I've never (knock on wood) had any problems shifting whether hot/cold or moving/not moving. So far so good with ~1800 miles on the car.
That said - I don't think your issue is tranny alignment - or else changing external things wouldn't fix it for a while.
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