Quad tendentious, calf/hamstring pain advice?

I play competitive college ultimate Frisbee of which my season just ended. Ultimate requires extreme speed and endurance and can be very rough on an athlete s body due to the amount and force of directional changes which occur throughout a game. Ultimate tournaments can consist of around five to eight 90 minute games over two days, of which a player will usually play half or more of the points.

About a year and a half ago I developed pain where the quad tendon connects to the patella just at the upper edge of the knee cap on both knees. I played the entire season, not practicing between tournaments, icing and taking ibuprofen, to lesson the pain. At the end of the season the pain was excruciating and I finally saw a doctor, started taking prescription anti inflammatories, and went to physical therapy. I stopped exercising all together for two months and attended PT and felt little progress. Throughout the fall I babied my knees and slowly build up lower body strength until the tendentious was no longer a constant issue. I consistently iced and stopped conditioning whenever the tendentious would flare up. Over the winter I did distance running, plyos, lifting (including squats, straight legged dead-lifts, box squats, leg extensions, leg curls, wall sits, and calf raises), mid distance sprints, short distance sprints, deep water running, speed ladders, and lots of abs.

As the current season progressed the tendentious came back, however not as severely as the previous year. If I take heavy doses of prescription anti inflammatories prior to a tournament I can make it through, but I know it is just delaying the effects of the over use. During this season I began to develop mild pain in the upper calf behind both my right knee ( I think it is where the hamstring and calf tendons join). If I wear a patella knee brace it helps to prevent the pain behind the knee and maybe slightly helps with the tendinitious.

I feel like an old man. If I am not warmed up a sudden use of the knees, such as jumping and landing with bent knees or going from standing to sitting, can be very painful. I often wake up at night because the tendentious pain requires me to change the positioning of my legs from straight to bent or bent to straight.

Does anyone have experience with this sort of injury?