Move the seat back. Just try it. I bet that's the one thing that has probably impacted your knees the most. Just a guess.
As your knees get back to normal, focus on high cadence, 90+. And trust me, once you get use to high cadence you will never look back.
Good luck I hope you heal up!
"Life is not a journey to the grave with the intention of arriving safely in a pretty and well preserved body, but rather, to skid in broadside thoroughly used-up, totally worn out, and loudly proclaiming: WOW WHAT A RIDE!!!!"