Regarding your concerns about where the rubber mount is lining up on the support, I have one question, are the motor mounts swapped? There is a specific left and right. You CAN swap them around AND the engine/tranny WILL sit down in the compartment. If they're swapped it will move the everything forward. That would change where the tranny mount lines up on the crossmember.
At the risk of public embarrassment, I admit that I found out when I originally dropped in my EFI 5.0 and AOD. I wanted to check a few things for fit and then measure to fab my tranny mount. I was thrilled at the space I had from the back of the engine to the firewall. When I climbed under the car something just didn't seem right. I did some double checking and lifted the engine up, removed the mounts and checked them. Dooooooh! :roul Ford conveniently stamped the right mount with a big "R". Unfortunately, if you don't both to check, it doesn't matter! :char When I put them back in properly and dropped in back in, it moved the engine back towards the firewall into it's proper position, and subsequently the tranny (and it's mount)! :roll
With all that said, if you're SURE the engine mounts are on their proper sides, IMHO, I wouldn't sweat it!