['68OrangeSunshine]

2 or 3 things crossed my mind since we looked at this problem:
1] The nose cone on the replacement unit was a little different.
2] If your flywheel bolts were not torqued to spec, could not your flywheel have shifted slightly? That might cause a problem like "crazyred" sketched out.
3] With the flywheel front cover in place, that gives you a ~1/32" shim there.
Give me a call if you want to torque down the flywheel. I'll back up the harmonic balancer nut.
It sounded like a mechanical, rather than an electrical problem.