As everyone has said, the more you ride, the better your conditioning will be, that's for certain. Relaxing on the motorcycle comes with practice. As you get more relaxed, doing things like riding with one hand, and changing your position in the saddle will also help in long ride comfort. All of the above take time and practice.. When you are riding, make a point to relax your grip on the bars, and rotate/shrug your shoulders to stretch the muscles.
If you find yourself wishing to be a little more upright, consider handlebar risers that bring the bars back and up. I like Heli-Bars, but there are other good ones too. If your butt gets sore, try a Beadrider seat cover or a sheepskin. These are economical ways to improve your comfort over long rides. A set of highway pegs are also very handy to give you a whole different seating position, stretch those muscles, and change the pressure points on your butt.
To stay cool on long rides, I prefer to wear undergarments that are designed to be made wet, and act as evaporative coolers. Your current jacket is fine for even the hottest weather, if you wear something like this underneath, and carefully control the airflow through it. You don't want too much airflow, because it will dry out the undergarment very quickly and you lose the cooling. Mesh jackets are fine for temps below 90 degrees, but when it gets really warm experienced long distance riders generally wear full coverage gear with adjustable vents. Here in the desert southwest, I find wearing my mesh jacket in 100 degree heat dehydrates me very quickly. This is something you will have to experiment with for yourself. Check out LDComfort gear for examples of the undergarments.
Ultimately, your comfort level on longer rides comes down to your conditioning, and setting up your bike so that it a very comfortable place to be. For example, I can ride my ST for well over 30 hours, stopping only for fuel and bathroom breaks, which I manage to do in less than 10 minutes. At the end of a 30+ hour ride, nothing is sore. Tired, sure... but I don't hurt.
Garry