Mounting everything relative to the engine would definitely help with all the tensions and stresses put on the different components. Plus, it sounds like it wouldn't hurt to upgrade your engine/tranny mounts with something a little stiffer. Less movement in the rubber bushings means more power to the ground --> more efficiency, right?
And you might want to think of some simple spring powered tensioner for the chain. That might help immensely with the skipping problem. And you'd have no problem using something like this to let the tensioner sprocket align with the chain:
Since it does not have to transfer power and all.
