I know nothing about anatomy, etc. But, being 50+ and riding between 400-600 miles / day when travelling (my commute is ~2 miles) I do have some experience riding distances (I've got an IBA number around here somewhere). I sometimes get pain in my knees (I was young once and never really thought I'd get old). I take Aleve, one pill for 8 hours, yada yada yada. I ride all year 'round but travel much more in the summer months. I've noticed that pain is much more likely in the spring than in the fall, so I suspect there's some level of "getting used to it" is going on. Couple of things:
1) Try removing the bar-backs / risers. A forward lean may make things a bit more comfortable. Try it for a week or two and see if that helps. If not, you can always put them back on. If it helps a little bit, you might even try getting some S or RS bars to see if that helps more (1100 RS bars are a bit wider and higher than 100 RS bars).
2) The Corbin seat. It will be much more comfortable if you're leaning forward a bit. I had a Corbin on an RT and found it quite, "hard". Now I have it on my RS and it is like a whole other seat. Much more comfortable
3) Try placing your feet on the passenger pegs from time to time, or sitting on the back of the seat for some distance as you ride. These are techniques that many long distance riders use.
4) Yoga with your main squeeze, cannot possibly be a bad thing!