Can you take a picture of you on the bike? Might be something obvious with the position. Easy way to check seat height is to put the crank at the bottom, parallel to the seat-tube and put your heel over the pedal-spindle. You should not be able to touch the pedal with your heel. Check out
Dave Moulton's bike sizing & fit guide.
Also gearing depends upon speed and RPM. If you're in the middle-ring going up a 10% grade, that's too big of a gear. Leave your pedal-clips loose to give your knees and ankles plenty of wiggle room. Don't push hard on the pedals, you should feel like your legs can't even keep up with the bike; like they're freewheeling in the forward direction.
Be careful, don't push it. It doesn't take much to cause permanent knee-injury. Get your position checked out by a shop with FitKit and get a computer that reads RPMs so you can stay above 85-90rpms the whole time...