Have a good look at the tailshaft bearing in the box as well. If its a TH350 you can take the tailshaft off with 4 bolts. The vibrations could easily have damaged the bearing as its only a white metal one.
With regards the engine angles, if you set the carb flat at ride height this should have left your gearbox tail flange at 3 degrees down (std inlet manifold angle). Your rear axle UJ flange should then be 3 degrees upwards. There is a bit of leeway but that's what you should be aiming for.