Although you mentioned the front of the shaft was "heated/warm", may just be heat transfer from the tranny, exhaust?...

Have you looked at the converter/flexplate bolts, inspection cover for any signs of contact?

Sometimes we make changes that we think have no effect on problems, and neglect to mention them when asking for help, have you made any suspension mods? a different pinion yoke perhaps? transmission yoke change during the rebuild? I'll assume you checked the rubber tranny mount?