Something sounds odd about this situation. Have you come up with any solutions since you have posted this?
This forum has been slow the past couple years unfortunately. I think much of the old crowd has flown away to the social media scene.
In regards to the engine and trans, they should be 100% interchangeable as the engines both have BOP (Buick, Olds, Pontiac) bolt pattern.
To start, I would verify that your frame is lined up with the body. There are two alignment holes where the frame bolts up to the body at the base of the firewall. This is a basic check you should start with before messing around with shifting the engine. In other words, the engine sits in the frame...make sure the frame is lined up first.