I went to see my primary physician as well as my physical therapist (both of whom are part of the Sports Medicine office at Chelsea Piers). The bad news: I have very tight hamstrings (I knew that), a tight TFA, a tight IT band, strength imbalances, weakness, pronating feet, and I am horribly out of shape (OK, I added that last one). The good news: these can all be fixed and or dealt with.
My PT, Samantha Reenders, DPT, (who happens to be extremely attractive) told me that I have to stretch my hamstrings. She showed me how to utilize a contract/relax technique with a towel to trick the muscle into lengthening more than it would like. In addition to that, I should continue to use the foam roller as I have been. Then, for strengthening the muscles outside of the gym, I can use a thereband for hip abduction (think reverse Thigh Master) and unilateral, shallow squats on a step or a low platform.
In parallel to the PT, I can keep going to the gym, which will keep my moderately sane. I am going to avoid anything that hurts my knee, such as deeper squats and high step ups, but should be able to perform exercises that require less knee flexion such and Romanian Deadlifts and Good Mornings. Just taking it a day at a time now, but for the first time in a long time, I am actually confident that my knees might one day function without pain.