The rear mount of the trans has to work in conjunction with the engine mounts. Hang your engine and tranny from a hoist and place it into the engine compartment and make sure everything fits - alternator, fan, headers, steering box location, etc. Remember that the engine carb base should be relatively level. The oil pan should have enough clearance to avoid being crushed when going over potholes and into steep driveways. When all these things are taken into consideration then you can pace your crossmembers for your engine and tranny mounts.
As far as clearance with the floor board tunnel as little as an inch is all that is needed to account for engine and tranny torque flex.