I have had a T-5 in my '50 and now a Tremec3550 and was able to use a standard flat floor without a problem. I also replaced the rear motor mounts but never had a clearance problem. The only other thing that comes to my mind is the condition of your cab mounts. If they are in poor shape, replacing them may give you some additional clearance. Good luck - the 5 speed is a great set up!
