Get fitted on your bike. If you have been, get refitted. Let 'em know exactly what's going on. Just say, "after mile 30, my right/left knee starts to hurt, I'd like to find a diagnosis." It's surprising how little you have to change something to have a huge impact on your ride. My right wrist has been KILLING me lately, I'm going to go with a shorter stem when I get the chance. I initially thought my stem might be crooked, but it's pretty damn straight. My right hood might be off too, I'm looking at all my options.