When I first started reading I had a number of suggestions, then I kept reading and it sounds like you have tried them all. From my experience (me knees are extremely fussy) different insoles have a significant effect, so the fact you have tried superfeet and found no relief makes me wonder if it would be worth triying others such as the blue specialized insoles. I went through 4 before I found some that worked for me.

Another thing That might be worth a try is different shoes. I find for some reason (dont really know why) no amount of adjustment and messing around will get rid of the knee pain I get wearing sidi shoes. I think its becasue they are just a little narrow for me. IME good knees start with good feet. It took a year for me to try different shoes and my problems (IT band pain mostly) went away fairly quick.

Dispite the above, it sounds like you have tried a lot already so its possible this has nothing to do with the equipemt you are using or the fit on the bike so I think you are doing the right thing in seeking all the advice you can.

Good luck and dont give up, it took me 3 years to nail my probelems but i got there in the end