This has been a frequently discussed topic. If you've flipped your axles and still have clearance problems, then you need to lower your truck. Can't tell you how, other than others have done it. I think DC actually has a kit. Myself, I bought a new 5er. They seem to be doing a better job of designing them now for 4X4's. I'm sure someone else will jump in with advice on this one.
Good luck!