Pain in the Tailshaft!

Have you considered that you may have installed the engine brackets on the wrong side of the lugs? That's about a half inch right there.....
The trans mount is in the right location, for any trans that the truck came with. If you move it, you will have driveshaft length issues.

The bracket should be bolted onto the rear side of the lugs, which will tug the engine forward.

I'm pretty sure engine brackets for cars are different from trucks.