Chevy made several different styles of rear transmission mounts; it may be possible to give yourself the minimal clearance by switching the rear mount. When I converted from a two-bolt mount to a one-stud mount on my TH350 it lowered my trans about 1/2-inch.
Also make sure there are no spacers in that rear mount that are elevating the engine. A previous owner could have been trying to adjust his driveline angle.
