I started cycling from running. Then I was doing both and doing great. Then the knee pain. So I stopped running. What I found out, was the cross training made me better at both. My cycling speed went down without the running. I just added running back in and I know it will make a huge difference. The muscles you use are very different but complimentary. Try it. People also strongly recommend weight lifting, but I don't like doing leg exercises.

PS I was running 6 miles at a 9min mile for years (like 25 yrs) When I added cycling, I got down to an 8 to 8.5 min mile without even trying. That is a HUGE improvement. Similarly, my cycling speed is currently suffering but I am working (running) to fix it!