I spaced mine out with a 1/2" spacer (mounted flat to the door, no CSII bracket), moved the power window motor back a 1/2" and everything cleared. I did have to rebuild the botom of the doors since I was ditching the CSII assembly. I am currently rebuilding the old rebuild to make everything clear my roll cage (pics soon!).
It's tight...you have the window motor to one side the stop guide on the other. The actual window wasn't a problem.
It seems magnet width is more of the problem than depth.