So, in case anyone is out of the loop -- I am recovering from knee surgery. The particular culprit that caused all the problems is called "Patellar Tendinosis". Go ahead. Google it. You'll find hardly anything because it's pretty rare.
Here's the best summary of the injury that I've found (in case you want to use it in a book or something):
http://www.tendinosis.org/injury.html No one really knows what causes it, is what you'll get. The current guess is that there is a maximum "healing threshold" in which the body can repair damage normally. If you are bloody minded, stubborn, and a fool (like me), you can push your body past the healing threshold, and instead of healing things normally it just throws whatever tissue it can at the injury -- bits of bone instead of patellar tendon, whatever -- and you end up with Tendinosis. The problem is once the tendon heals incorrectly it never remembers how to heal correctly again. It's almost like the Prion problem (prions are a lower state of energy than like substances in the brain, so once you have a prion in your brain, your brain chemistry starts sliding down that low-energy slope). Actually, tendinosis is completely different than that, but I keep getting that simile stuck in my head.
Anyway, they fixed it by cutting out the "dead" or "mishealed" part of my tendon, and letting it regrow.
Things are doing well so far -- off crutches, in PT, healing ahead of schedule -- but I have a long way to go to full recovery.