I am a PT in the Denver area, and have a couple of suggestions. First you mention all kinds of stretching/soft tissue work that doesn't seem to be helping. Have you also been doing strengthening? Is your PT picking up on any muscle imbalance? I don't give much credence to a weak popliteus. It sounds like extension is the main problem. Try this, find a position/activity that will bring on almost immediate pain. Use this as your "control" variable so to speak. Now, sitting on a table or high chair, (feet off the floor) fully extend your knee with a really hard contraction, hold for about 5 seconds and repeat 10-20 times. If your pain increases with each rep then stop, if there is no change or it gets better keep going. There is no magic number to do, and being that you have had this for a long time, the "ideal" number of reps may be high. Anyway, do a bunch, then repeat the "test" that produced pain to begin with and notice if there is a difference. In general I have seen repeated extension help more often than Flexion, but if extension does not work, try repeated end range flexion. End range in both direction means getting to the end of the joints natural range of motion. I should add, that your PT can also help in this area. If the extension seems to give a benefit but not fully take the pain away, ask your PT to do extension mobs with overpressure. If they don't know what that means find a different PT.