I just had two long weekends. Went to Birmingham from Panama City for the AMA Superbikes. Made one stop in Troy for gas, so the trip was two stints over 2 and a half hours. I was very stiff after, and had some pain at my tailbone and between my shoulder blades. On the way home, I stopped every 60 to 90 minutes, just to get off and stretch.
The next weekend I went to Atlanta for a college friend's 50th birthday. Made 3 stops on the way up, 5 on the way back, although 2 of those were to get into or out of rain gear. Still some tailbone soreness, but no shoulder blade tightness this time.
1350 miles on two weekends.
If the seat was better, I'd be happier with longer runs. Good seats are serious $$$, though, so it'll be a while.
Things I've done to the bike for comfort: A set of risers to bring the handlebars up and back a bit over an inch, so I don't rest as much weight on my hands; heavier bar ends to quell vibration; cruise control so I can let go of the throttle grip (FJR's are notorious for a heavy throttle spring); and "highway pegs" about a foot forward of the regular pegs so I can move my feet forward for knee relief.
If you're gonna be on the bike more than an hour a day, then being comfortable on the bike is extremely important. Stiffness and soreness, aches and pains, will detract from the experience, but more importantly, they will distract your attention from the riding, and that can lead to bad things.