The first thing I'd try is raising the seat by quarter inch increments. When the pedals are level, your tibia should be straight up and down, as a kind of guideline. You should have a slight bend in your knee when your leg is straight down as far as it will go. I've heard that knee pain is often due to the seat being too low, (kind of opposite of what you'd think) so I'd start in that direction.

Nanci