I went for a professional fit and the guy put two 1mm shims on the right pedal, none on the left. As small as that seems it made a big difference in knee pain. The guy was amazing, raised my seat 4mm, put 2 shims on the right pedal, shifted my seat back 3mm. I was really surprised. My right knee now travels in a straight line (almost). The problem is that if you buy a production bike you get the BB that use. That same BB is there on all sizes and it doesn't matter what your body measurements are. The shims helped to compensate for that.

Find a really good LBS that has a trained and experienced person who can give you a real fit. If you are still out of alignment after that it's not the bike so see a good massage therapist who concentrates on body alignment. And if that doesn't work I guess your just warped