I think it isn't possible to change keybindings for character movement ingame, however you could try using JoyToKey to map controller buttons to keyboard/mouse input, but I haven't tried it.
Otherwhise, I'd recommend exercising regularly if you don't already. I used to feel a lot of pain on my shoulders and arms after playing for a few hours, but it improved a lot after I started going to the gym and lifting weights, to the point where I don't feel any pain anymore.