I think I may have figured out the drivetrain angle issue.
I think the siderail section of the frame on my truck may be taller than the one on my donor truck, I'll have to stick a tape on both frames to be sure. From some information I found on another forum, it looks like my crew cab should have the taller frame vs the standard cab donor truck.
It seems that if my truck has a 7.2" tall frame and the donor truck has the 6.06" frame, it could cause my problem. So, if that ends up being the case, I'll just build a 1" spacer to go under the transmission and then flip my carrier bearing cross member back over and call it a day.