1. Am i going to have enough clearance between the body and T-case if the T-case is that mush higher? (I have the body off so I cant tell)
If you have your body off, I would make your t-case 1/2" above the bottom of your frame and then cut out your tranny tunnel and build a new one. That way you can build a flat belly!
2. Do you think that that tilting my T-case up one 1" is going to hurt anything, I.E oil to motor, more stress on motor mounts... etc?
Loosen your motor mounts before you do it. Then retighten them after you have it positioned. I've seen people clock their entire drivetrain 10* to get a flat belly.