Knee Pain from Recumbent Bike

It's been awhile but the pain continues. I got x-rays and they were normal. I've been doing pt to correct patellar tracking for three weeks now and the pain when sitting and standing in place have gotten better but the pain when walking has gotten much worse in the past week and a half. I am seeing the ortho on Monday. Just trying to figure out what it could be. We have been working on muscle strengthening and stretching and working on any tight areas such as the ITB. My strength and flexibility have increased and I can do the exercises without a problem. The main issue is the increased pain when walking  and going up and down stairs that started after pt. Can't figure out what the cause of this is. The pt seems to not think I have any issues with the ligaments of my knee and cartilage. If anyone might have any other ideas, I would love to hear them.

I started to feel pain in the quad tendon area above the right knee and the medial retinaculum area of of the the right knee. Sometimes the entire knee cap just feels a little sore.  I've been using the "R.I.C.E." method (rest, ice, compression, elevation) and I've stopped all physical activity. That would include bike riding and lower body strength exercises and stretches. Its been over two weeks. The dull pain is intermittent and feels worse if I am sitting in a chair for extended periods of time. I am not sure what the exact injury is but am trying to self treat it and see if that helps. I've read that after 6 weeks if that does not help, to see a doctor. My main question is, if I still feel any sort of pain, should I try to help the injury by warming up the muscle (say using a heating pad), and do proper stretches and strength training of the areas surround the knee and general lower body? I'm just not sure if part of "self-treatment" is stretching and strengthening of the area involving (either directly or indirectly) the injured area. If so, should I then ice the area? Also, should I wear a knee stabilizer if I do try to stretch or do strengthening exercises?