Muscle imbalance is the usual reason for knee pain. IME lack of exercise is the ordinary reason for most other muscle and joint pain. You can fix all this by joining a gym and working out 2-3 times/week. If you want guidance for what to do there, this book is as good as any, better than most:
Body By Design Book: Make Your Dream Body A Reality!
I don't think you can bicycle these problems away. Cycling several times a week is still a good idea because it will work out the muscles which you are bringing to life in the gym. For glute work, it's hard to beat squats. To equalize leg and glute muscles, one legged presses on a leg sled or leg press machine are the way to go. To equalize knee muscles, the leg extension machine, operated only through a 120°-180° arc, is the best. For upper body pain, dumbells exercises rather than using barbells are the way to go.
If the pain in your shoulders is from impingement:
Shoulder Impingement Syndrome: Symptoms, Treatments, Causes, and More
then there's a book for that too:
http://www.amazon.com/dp/B003ICWIUM/
I've been using Dr. Kirsch's treatment and it has worked, when no other PT had much of an effect.