Time For a rebuild

Ok help is needed!!! Had a good friend come over tonight and we pulled the trans and engine out. Yes pilot bushing is still in the crank but just mocking up the engine and trans on the floor they went together lickity split. We then put them in the car as a unit, was not to bad at to do really. Got the trans in place and on engine mount bolt half in, could not get the other side engine mount bolt in. Dropped the trans mount and removed it from the trans, lined up the mounts and slid the bolts through. Went back to the trans and it is out 1/2 inch. Trans will not slide over. Are the engine mounts different on the 5.7 and 6.1 on the alterktion?? Any help would be appreciated..

Trevor