Have you considered getting a professional fit on your bike?
I always went with what-felt-right, and was having chronic knee pain. It seems a little silly to pay someone $150 to shift your seat, cleats and bars, but it made all the difference for me!
I was doing yoga, therapy stretches, making an appointment to see a surgeon... but a fitting with Nate Loyal in Santa Monica cured my knee problem and now I can ride as long and hard as I like.
If you're in the LA area, this guy is excellent:
http://www.nateloyal.com/