Sounds like you've gotten a lot of good replies. I just wanted to add my two cents. Ditto on the right bike fit. My bike fit session was about more than making sure the bike fit my body correctly, but also about my position on the bike and if I was pedaling efficiently, etc. I learned I was putting way too much pressure on the handlebars, which can cause problems like neck and shoulder pain. You are supposed to put minimal pressure on the handlebars and use your core more for support. Also, move your position on the bars from time to time.

Just before my bike fit, I had done my longest ride I had ever done on that bike, about 65 miles. I was dying on that ride, which is what made me get the bike fit finally. I can't tell you what a huge difference the right fit made, plus the knowledge of proper form on the bike, etc. I don't think every bike fit person will necessarily work with you on form, but if yours doesn't offer any input on that, you could always ask.

Also, ditto on the right saddle. You really have to try several to know what works for you, and just taking a spin around the block won't necessarily tell you. If it's clearly NOT the saddle for you, a spin around the block may tell you, but if it's a maybe, then you really need a good distance ride or two or three. There are bike shops that will demo saddles, but you can also buy saddles at performancebike.com and they have a money back guarantee. You can return anything any time even after you've obviously used it. Check on that to make sure nothing has changed, but that's how I tried some of my saddles. You have to pay for them up front, but then you get money back on anything you send back.

Another tip is to get up and out of the saddle from time to time. Sometimes when I'm climbing a lot on some mountain road and there's no stopping at signals or anywhere for a long period of time, I will stand up and pedal fairly easy for a little bit, just to relieve pressure on the bits ... as well as to use different muscles for a little bit. I can't do it for very long on a climb, but long enough to help the hoo ha out a bit and give my overworked muscles a break. I'll do it on any long ride where I need a break from the saddle. Often when people stand, it is to go faster, but that doesn't have to be the point. You can stand and keep an easy pace and not tire yourself out too quickly (which standing tends to do). Also, you can get out of the saddle on downhills, but I think you have that one down!

I often get a sore on my skin when I do longer rides (down in the nether region). While I still wonder if there's something better I can do (different saddle or something else) ... I find that using two products down there helps. When I do a long ride (or am sore because I just did a long ride), I will put either Neosporine or A&D Ointment directly on my skin, particularly the actual spot that gets irritated. Then I will put Chamois Buttr in my shorts. My friend and I call them "layers". Base layer and second layer!

A few times on a century I brought Chamois Buttr with me and added it at a SAG stop. I learned that doesn't really work for me. I don't know what it is, but I guess I just get "too" slippery or something and I find I'm even more uncomfortable than I am if I just leave it alone. So I do my base layer and second layer before the ride and let it be after that. But that may not be the case with you. You have to figure out what works for you.

Once you figure out bike fit, saddle and learn to stand from time to time ... you can start building up miles to where you body does start to get used to being on the bike longer and longer. I would still love to be more comfortable on the bike than I am on long rides, but it's a lot better than it used to be after all of the above.