I think the recom. of getting a PT in the loop is a good one, and perhaps also an orthopod.

I had severe back and hip pain (both on and off the bike) that didn't go away after a cycling accident. It turned out that it was caused by a poorly healed fracture that left me with a 3 cm leg length discrpancy, twisted hip, and inflamed SI joint. First it took a really good orthopod at our medical center to diagnose the problem. Next he sent me to a really good PT that gave me back strengthening exercises, and physically manipulated my SI joint until it was healed. She also gave me inserts for my shoes to wear on the short leg side. Then I went to visit with a cycling biomechanicist (Tom Slocum of High Sierra Cycling) who measured the impact of my LLD (and also twisted hip) on my pedal stroke, and made me a custom crank set that compensates as well as possible for my biomechanical issues.

If you are willing to travel, you might want to visit Andy Pruitt in Boulder, who runs a clinic specifically for cyclists with biomechanical issues, and he could also give you a therapeutic bike fit, which is diff. from the fits you can get in a normal bike shop.