hip and opposing calf/knee/ankle pain

I've got pretty chronic pain and tightness in my right hip/back and the opposing leg's calf and ankle (and I suppose foot too, under my big toe.) It's been going on for a few years now. My knee has always been able to "pop" from side to side since childhood and I never thought much of it. I don't know if it's related to this problem or not but it, too, has been hurting recently. The painful calf is a little larger than the other calf and the muscles around the painful hip/lower-back are larger than the non-painful side. I've asked my doctor about a possible leg length discrepancy but he insisted it wasn't the case just by looking at my knees from a distance. I'm pretty active and run three or four days a week so I doubt it's related to non-use (in case it helps, I'm 5'9" and 160lbs.) My doctor hasn't been any help and I don't know what to do or who to see to help me resolve this. Thanks for any guidance.