John,
Quick queston for you, is the pain feel as though it is in your hip or does it originate from your hip flexors? Reason I ask is, most "hip pain" complaints from riders is due to weak hip flexors. This pain becomes pronounced when the knees are drawn/bent toward the chest/upper body, with resistance applied. The resistance in this case, is either the wind against the chest and/or the G-force from the machine, usually the combination of both. Additionally, when your foot turns outward(external rotation) while the hip flexors are engaged, additional stress is being applied. If this description is painting a clear picture, you will also see that highway pegs can exacerbate/worsen the problem.
So what is the fix? In order to extend the legs, you obviously would need to either move your position in the saddle back and/or move controls forward. Highway pegs should allow the legs to extend out with a slight bend in the knees in order for the legs/hip flexors to relax. Lastly, strengthening of the hip flexors. This combo should allow for relaxed riding and mobility after getting off the scoot. I would suggest a strengthening exercise that isolates the hip flexors, while providing minimal or no stress to the lower back. IMO flutter kicks would be an example of a BAD, BAD exercise. I personally would prefer to do hanging leg raises, which do not involve the lower back.
Hope this helps, I tried to keep this in laymens terms, if any clarification is needed, give a shout.
SOKOOL