i hear your pain. slvoid - this all started during the century tour, right?
i have, for a year now, been trying to dial in my bike just right for me. seems like i adjust one thing and something else hurts, then readjust and another thing hurts. don't forget to adjust fore-aft position on the saddle - i've found that really can affect the stress on the knees.
my other advice (keep in mind i haven't discovered my perfect sweet spot yet) is to make small ajustments, give it two rides of somewhat long distance, then adjust again, ride more, etc... keep a journal of what hurts at what position and at how many miles. hopefully you can get it just right.