I don't know about your situation so much, but I have one foot that pronates heavily (just learned in PT that it's actually a hip problem to work on), and if I don't wear insoles with serious arch support, I get pain. Also, if you're not clipped in, all pedaling is powered by pressing down, which might be irritating a tendon or something. Maybe new shoes would help, maybe insoles. I dunno, but I wish you a speedy solution.