I havent read the whole thread, my apologies if any of this has already been said:
1) Your running mechanics might be off. Get them checked out by a good running coach. The POSE method may be something worth looking into.
2) You should start squatting and build up the ligament and tendon strength of your knees. Emphasize proper technique, namely keep your knees out so that they run parallel with your feet when viewed from above, and keep your weight on your heels. Get the book Starting Strength (its torrentable). extensions are not the way to go here, for why google `leg extensions eric cressey`.
3) Gluteal activation work. Supine bridges.
4) Glute-ham raises, although most gyms dont have the machine needed, it is possible to do these just with someone holding your ankles.
5) Massage. Deep, hard massages of the IT band, quads, hip flexors, hamstrings, and calves. A foam roller will save time.
6) Taping your knees will allow smoother pateller tracking and could help..
7) And of course stretch everything out, dynamic pre workout, static the rest of the day.
8 ) Get your posture checked out. Read ``neanderthal no more`` on tnation.
to pop in and see you!! Or maybe you'll be neighbors with me and Slushy 
