To check for clearance we reattached the drivetrain in it's original location of crossmember to transmission tail housing.
It turns out there are only two issues.
1. T/case top is contacting the bottom of the cab where the e-brake cables are held:
2. The top of the t/case front output section is not touching but is very close to a body rail:
sounds to me like a simple 2" body lift will fix that. With the body lift you can solve three problems at once. Two problem you have now and prevent a problem you can have in the future. The body lift will give you clearance for the drive line and tires. Since you have the body off the frame change the rubber body mounts and install POLY body mounts and you will never have to worry about the rubber ones rotting off.
I also like the feel of the poly mounts.