I've been struggling with knees too. I'm doing an MS150 this weekend and I'm rather concerned about how my knees will feel on day two. I've been trying to work up to it and have been doing a 40-60 mile ride every weekend for the past couple of months. I mostly feel ok on the ride, but my knees are still always a little angry a day or three after.
I've adjusted about everything on the bike multiple times and watched a lot of fit videos. I've also used myvelofit and got everything in the green. I'd try a shorter crank next, but don't want to make any big changes this close to the ride in case it makes things worse. Maybe I just have bad knees. I did this ride 5 years ago and my knees never complained, but I'm on the wrong side of 40 now.
Anyways.. I use a knee brace and always take a long soak with salts afterwards. I don't know if either of those actually help. I've never had any swelling. Just soreness above the knee cap.