Ya, this IS all a big shot in the dark without assessing your legs. I agree with gonzo as far as the possibility that you are having a quad imbalance in relation to lateral and medial vastus ratio but if your hams are weak you could also be having problems. If I were you I would spring for a single evaluation and recommendation session with a good PT that specializes in sports/orthopedic conditions. It's hard to give you much good advise without a thorough assessment.
Good Luck.
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