I can't ride even as long as you. It isn't the bike, it is just my crappy body. For me it is neck/shoulder/back pain and my hands go numb. No amount of adjustments can help all that much, it is just me. I suspect some of it might just be you. If you have long legs, it might help to get a taller seat or lowered pegs. (I have short legs and had to lower the bike and seat, and wear tall boots).
I will say that someone on a new (at least to them) bike *is* going to have much more pain and problems until they get used to the exact riding position. With repeated riding, you will tone the muscles that support the various positions. I haven't ever had leg/knee pain, however, but that is just me.
When I first got the C14, I spent a lot of time trying to change things to help with my back. Even so far as to adding pseudo highway pegs. But after much riding and time, much of that pain disappeared as I became more "in shape for riding." I haven't even used the far pegs in many years.
My recommendation would be to give it more time before making changes. You might also combine this with stretching/range of motion and even toning exercises in the areas of your body that suffer. Riding a motorcycle isn't a "natural" position we take in everyday life, for sure.