I can ride 100+ miles and really not have any discomfort other than muscle fatigue. That didn't happen overnight but took a while to get the fit right and also the proper equipment for me-saddle, shoes, shorts, etc.

My guess is there are some fit issues and/or your bike is transferring a lot of road noise to your joints. From personal experience I'm thinking your reach-top tube/stem might be too long??? What type of frame and fork is your bike? What type of wheels do you have and how much pressue do you run in them?