OK, since the T-Nation requires more information, here it is. My knee problems are a result of 3 things (1) Compromised joint stability (2) Muscle Imbalance & (3) Poor exercise form. I'll cover each of these contributing factors in order.
My right knee track excessively to the right in-part because I had some actually a lot of cartilage shaved from that part of my knee joint.
I made a potentially bad situation worse by continuing to squat with an excessively wide stance. This led to an overdeveloped Rectus Femoris & Vastus Lateralis. Not to mention a severely underdeveloped Vastus Medialis.
It was so obvious that when the therapist saw my quads she was really amazed (at how unbalanced they were. I always wondered why I never had a good "tear drop" visible in my quad. Well this imbalance was the answer ? the Medialis is what gives your front quads that "tear drop" appearance. My Lateralis was so much larger and tight that it was just a matter of time before my knee cap tracking was compromised.
I also had very tight hips, and hamstrings. Therefore I've spent the last 9 months increasing my lower body flexibility & strengthening my inner quads. Due to my knee situation I was advised not to attempt to squat but that if I must I should do "bodybuilder" squats & be very careful of my foot placement. I was also told that the combination of tendonitis, due to my earlier surgery, and in-line squats would be a potentially painful combination - which it was!
All of this information led me to my original post. I requested effective substitutes for squats not a diagnosis of my knee problems. But for those of you w/medical training or similar experiences feel free to conjecture away.