Your original injury sounds more like an injury to the patellofemoral joint rather than tendonitis. The combination of a direct blow to the patella (kneecap) and the symptoms of stair pain and pain when sitting for long periods of time are classic. This is sometimes called "dashboard knee", it occurs in motor vehicle accidents when the knee hits against the dashboard.
It's unclear whether this is related to your current problems, even though the symptoms are the same. However, you certainly may have an injury to the articular cartilage of the patellofemoral joint that has now been aggravated by your new cycling program or it could simply be the cycling itself. Improper seat position is a common cause of patella problems. Be sure that your far leg is almost fully extended, about 5 degrees bent at the knee. Icing after riding can also be helpful. In addition, the use of a patella stabilizing brace for riding may be useful. If the pain persists, see an orthopedist.
Thanks a lot for the help, it was very informative. The idea of dashboard knees actually makes a whole lot of sense, after some thought I realized that during cycling I've nailed my bad knee on the cup holder a few times and the pain started after that. The pain had been getting worse almost daily so I think I'm going to set an appointment with an orthopedist.
Thanks for the help!