OK, you say that you mocked up the rear end without the engine/trans in and you can deflect the C beam (thats the beam that runs foreward and bolts to the trans at the front) up/down 30 degrees, it will move up and down because the trans is not there. to get what i am saying put a jackstand under the front of the beam to simulate the trans mount, with the front of the beam on the jackstand see how far you can push the beam down, heck, jump on it if you want.
what you want to do is mount the rear end (i assume already done), next mock up the engine + trans in the car so it is pointing directly at the pinion (and the pinion is pointing directly at the trans output shaft). you need to get everything-pinion, trans output on the same plane- so that when the driveshaft is in you have 0 deflection on both u-joints, like this =-=. this needs to be done first. only when you have your engine, trans and rearend mounts made and everything is lined up you can start to build your new shorter C beam out of steel tubing.
i know you are concerned about how short your driveshaft will be but with what little deflection rubber bushings will give the u joints will easily handle. just get everything mounted and lined up before making your new C beam.