In the last two years, I've done a lot of concerted effort at increasing my ability to stay on my bike for long periods. My work is paying off. I had back and shoulder and foot pain after an hour, sometimes less. I've had knee pain, but it's been less severe. No one thing has alleviated these problems. There have been many things. Taking longer bike rides, riding faster (to build endurance), lifting weights, seeing a podiatrist, and paying attention to the subtle matters of fit are the five most helpful approaches for me. I can't say what will work for you, but chances are, you can endure more and even incur less pain than you currently do.