I'll second the advice of our tandem riding friend here and tell you to seek out the help of a cycling coach or physical/occupational/sports therapist. Your insurance should cover that...even if not one consultation is pretty cheap.

I'd say just to buy the pedals and move the cleat all the way back since good MTB racing clipless shoes are very stiff. However, you sound like you've got a unique problem that a professional could probably help you out with.