Hey,
See Mr. Silver's LCL thread for a link to an article I posted on pelvic symmetry and cycling. Also check out cyclingnews.com 's Fitness Q&As. Steve Hogg (supposedly one of the best bike fitters) has a lot of info on functional and measurable leg length discrepancies and what to do about them.
Have you ever tried any shims under the short leg? Finding some compromise position means you're still stretching too far with one leg and now you've also hindered the performance of the long one. Some people even try 2 different crank arms.