FIrst I also agree see your Dr. What would it hurt to talk to them sooner rather than latter? It is only going to help you.
Lots of people have problems with knee's aching after riding. I have found several things that have helped me.
1. When I ride I don't walk the whole time and I post the trot. This allows my legs to work and not get uncomfortable in one position. You don't have to do it a lot. Just enough to loosen up the muscles.
2. I take my feet out of the stirrups once in a while and stretch them out.
3. I have tried for a year to get my fenders to twist. No mater what I have done they have continued to go back to a straight position. So either turn your fenders or get some swirl stirrups. It made a HUGE difference.
4. Lower your stirrups a notch. This gives you more room to relax.