My right foot points a bit outward due to a hip injury. I too have a longer pedal shaft on that side to prevent polishing my crank arm with my heel. I went to the fitter and after some Steve Hogg testing, shims were placed under the cleat on my left shoe. Also a heel wedge in my left shoe. You would think they would be placed in my right shoe.
Hope you figure it out.
Move to low or mid volume. Reducing overall load can make the work you do much more effective.
Might try dropping your seat a hair. I get the same inner thigh/knee pain when I ride my mtb suspension fully locked out (higher seat because eliminates the sag it was set with) or ride my rigid bike (I recently lowered the seat a couple mm and the next ride with no issue). The rigid bike may have been an issue because I ride with flat pedal and used to ride with shoes that have a thicker sole.