cryer, I'm the author of ShapeShifter. ShapeShifter does not modify anything in /System. Turn it off, log out, log in, and your're back to your defaults.

ShapeShifter does most of its work when you launch an application. On my test machine, it adds roughly 1/2 second to the time required to launch an application. Once the app has finished launching, the performance hit is negligible.

The issue I referred to earlier regarding window dragging and resizing is a bug, and as I said, I think I've got it nailed for the 2.1.2 release. I think it's a Tiger-only bug, but I'm not sure.