Sounds like you need to adjust the pegs. They can be a bit tricky to get them "just right." It's not a one size fits all deal.
I've had a bad back for 30+ years. PT's & Dr.'s tell me to keep my knees slightly above my hips when sitting, driving or riding. I suggest you start there. Remember angle of your feet / toes is also very important. I ride with my toes in a relaxed & a natural position, not pointing up too much or forward / down.
Also remember to change position back & forth between the two sets of pegs. At a safe speed, you can also stand up on the pegs for a few seconds, like on a dirt bike. You get some air in your jeans & cools your butt. Give the above a try, might work.
Obviously what works for some does not for others....I guess that is why the good Lord made us all different sizes and shapes...I have had 3 different types/sets of rider pegs on my last 3 bikes...I have never been able to ride using them for very long no matter how I adjusted them..The two bikes I had with floorboards worked the best on longer rides, but now as I get older, and my knees get a little tired, I just hang my legs down from the seat for a few minutes and then go back to the stock pegs on the F6B..Good luck and I hope you find a solution.....Back issues "suck", I speak from experience....Ride safe