Not sure how much help I can be, but I have similar problems. I run varsity cross country/track, and lift weights a few times a week and during the seasons I often get knee pain. I've found that doing light warm-ups followed by a couple mins of stretching really can help. That could work alongside any sport (including weight-lifting) i'd assume. I also stretch afterwards.
Also when you weight-lift, do you ever shift up your routine? I understand that working specific muscles is important given a specific sport. But mixing it up you not only strengthen all your muscles (vital for football I'd assume), but you can also give your knees a break by not doing so many squat reps.
I know I'm giving you some rather straightforward information here, but hopefully it can help a little. Also, I do know one senior on our distance team who would wear a knee-brace occasionally. I never did it myself cause I feel restricted w/ one, but it seemed to work for him.
That is about all I can think of aside from spending tons of money to see a physical therapist or something. Plus, I'd assume you don't need to take things that far.
Anyway, best of luck next season! Hopefully things improve!