I DEFINITELY recommend a pro fitting if you have knee or other joint issues. As a matter of fact, I recommend a pro fitting for anyone who gets clipless.

Ask your local bike club/s for a recommendation on a quality fitter. I would be willing to drive out of town to get a great fitting.

As far as specific pedals, I recommend speedplay for any knee issues. They have abundant free float (no spring tension), so your legs/knees can track exactly as they please.

As a runner, your feet and knees aren't locked into the exact same position with each step, you follow a natural gait. Speedplays allow the same thing when you pedal.