[OrrieG]

Side frame rails should be level and intake manifold carb plane level. IF you got the motor mounts and trans mount from the same company AND they did it right then you should just be confirming their engineering. If you got the motor mounts a little off then like Kim says it will affect the trans mount.

When you are laying under the truck looking for the mc location note the floor cross sills (braces) you do not want to cut those for your door. I moved my mc back so the floor trap door would be behind the front seat brace. Seat lifts up for access. You can see it could have went back probably at least a foot farther. The two bolts in the side frame behind the booster is the side mount for my transfer case/transmission mount. As I am typing this I just remembered it may be farther forward than yours because the transfer is close coupled to the transmission with the mount where the two mate up.

Don't know if this is solving any thing but gives you food for thought.