Are you stretching? What you are describing are typically a result of tight overused muscles. If your quads are tight from using them more than usual(like biking 6x/week) they will cause undue pressure on the patella as they cross the patella and attach below.They basically grind the patella into the cartilage below,eventually damaging it. So stretch out those quads. Back of the knee pain and swelling can be from bursitis, again from the hamstring tightness, again from all the new activity. These press on the bursa behind the knee, so do the hamstring stretches. Next with be the IT band. This will cause lateral(outer) knee pain. Do stretches for those.( Laying on side put the top leg off the edge of couch or bed and bring it up towards your head while letting it drop towards floor , keep knee straight) Oh yeah, and stretch....Any new and vigorous use of muscle will make them tight, and cause FRICTION. Friction is bad, for you and your bike.