You talk about wheeling, rub marks on the body, messed up shifter linkage adjustment, and a wiggle on take off...

When I first did my bodylift/drivetrain lift and the first section of the rear shaft was no longer in line with the transmission output, I had a "wiggle" type vibe on take off. That was why I later changed the drivetrain lift to 2" at the motor mounts and 1" at the tranny mount, which broght the whole drivetrain back in line up to the driveshaft carrier bearing. This eliminated that vibe.

If your tranny crossmember has been pushed up, you could have a similar problem- the first section of rear shaft out of alignment with the tranny. That could also explain why the shifter linkage adjustment changed. Try taking some careful angle measurements from the face of the tranny output flange and compare it to the first section of driveshaft. They should be at 90 degrees to each other.