I have this nagging pain in the bag of my knee.. its not anything too bad but its annoying and only when i ride for about 15 miles does it start. Its on my right knee and i noticed that when i ride my saddle might be too high because my right leg is used to doing more work and my bike kind of leans left. has anyone else had this problem? do you think lowering the seat would work so i can balance out my legs?

Your seat may be too high or too far back.

+1 on that. And turning too big a gear. I'd say aim for about 92-98 for cadence also.

Check out what Sheldon Brown has to say.