I finally went out and got my bike custom fitted, basically this means moving the seat around alot, both horizontal and vertical, as well as elevation. This placement turns out to be critical for long rides. I did a 50 mi ride two weeks ago (when the weather wasn't god-awful), and started to get knee pain as well as saddle sore. This indicated that too much pressure was on the perenium. Anyway I also upgraded the saddle to a 'deluxe' type from Specialized, called the Alias. Another person had the same issue and reported it solved. I rode the bike the 3 mi back to my house, and noticed the perinial pain was gone, but replacing it was pain where the thigh meets the pelvis, due to constant friction. I didn't have the special bike shorts (i was coming from work), so that would help). I also plan to invest in some special lubricants that deal with saddle sores. Basically the constant friction during long rides is a real problem. I guess previously i was just used to the bike's 'quirks', I'm not sure how I dealt with it, but the pain didn't used to be so bad. The extra pounds I got during the last part of grad school undoubtedly had a role. Anyway with the new saddle and proper fit I should reduce joint/back problems, not to mention problems 'down there' (numbness and sterility can occur in people who are on their bikes 20+ hours/week - the new saddles allow more blood flow and reduce this problem). Anyway here's hoping biking will not be a constant agony from now on.