I had been to a knee specialist before (several years ago), and they explained various things about my knee and what was happening, as well as strengthening excercises
Did you do these exercises? From people I know who have had knee problems (including needing arthoscopic surgery), they say that although the exercises are a pain and certainly not that exciting to do, they really do
however they couldn't provide advice on the best way to do aikido!
Maybe you can find a physical therapist who has done or is doing aikido?
Another way you can approach this is by looking at some movement therapies like Feldenkrais or Alexander Technique. I've been meaning to look into Feldenkrais myself...