The swap "shouldnt" change anything....but you never know. When i swapped in my 401, replaceing the 258, there wasnt any change to the driveline angle...but every swap somehow turns out different.
Did you have to relocate the positioning of the tranny/xfercase on the crossmember? did you use stock V8 frame and motor mount brackets?
It's more then possible the swap created a different drivetrain angle. You can self-diagnose it by checking the output angle and compareing it with the pinion angle. You want them as parrallel as possible. Dropping the xfercase will lower the angle of the output shaft....because it's pivoting on the motor mounts.
One last question, with the onset of the 360 swap, has your right foot become heavier? :?:
The 360 has ample power to force axlewrap on the rear axle. Obviously, when the pumpkin moves, the pinion angle changes. I've seen axlewrap trash ujoints and driveline yokes. That's something to also consider :-|