Brandon, I got your PM, but these guys have pretty much covered it all here.
As already stated, the rear framerails from the rear crossmember back are very flimsy and can move around quite a bit.
In my case, I had the opposite problem to yours, after all the additional welding and reinforcing I did to the rear rails, the heat pulled them up a bit. Nothing that couldn't be fixed by bolting the body back onto the frame tho. There's enough flex in those rails that they just moved back down as I tightened the body mount bolts.
By the framerails being "not tied together" he means there is no additional bracing connecting the left and right rails together.
The only thing that ties them together from the factory is the back bumper, and it only does a mediocre job of that at best.
Make sure to use a quality replacement body mount kit and pay careful attention to what bushings go where and how, because it matters. I used Prothane's kit, and was extremely happy with the quality and fit.
If you're 100% sure all the mounts are in the correct location, and there is no previous repair that could be affecting the area, you could consider trimming the height of just the rear bushings on the low rail to level things out for you, but I would try my hardest to find out what is causing the issue first.
Donovan