So I did a little digging around with the trans mounts on this thing. I also talked to vroomzoomboom a bit, and he helped me understand a few things I was missing out on.
I didn't even stop to think that the 4.0 & 5.0 trans mounts are different. The 5.0 mount is much shorter in height. The bolts to the trans are differently spaced. The Atlas is also much heavier than the 1354/4405 cases are.
My options as of right now (that I can think of) is to:
1) Build a tube/plate cross member myself, and use a stock 5.0 mount.
2) Modify the stock cross member to use a Mustang mount, that looks about the same height as a 4r/5r mount.
Using the Mustang 5.0 mount, all I need to do is weld a 1/4" plate to the top, fill weld the old bolt holes, and drill new bolt holes. It would hopefully gain 1.5" in height this way. Would most likely use a poly mount over rubber, even tho I prefer rubber.
As far as it being farther to the dr side now, I'm not sure if that's because the existing mount is bad (as Turdle suggested to me earlier), or if the engine mounts are off a hair, and it multiplied a bunch at the case end.
Jon, If I did clock it higher, I think the front dble C shaft will handle that angle change just fine. I want to see if just lifting it higher will help first. Getting this case up, over & away from those fuel lines is what I'm more concerned about. If I can get the clearance I want by lifting it, I won't have to clock it, and won't have to worry about the front driveline.
Last thing to worry about is the exhaust. Not sure if it would even allow the tail section to be raised that much. It is fairly tight & tucked in for ground clearance as is. The manifolds might say, umm... No, I don't think so buddy.
It would be nice to be able to just adjust the engine mounts to shift it back to center, and simple lift the tail section where I want it, and not worry about anything else. Yeah, Haha, like that would happen.