@mathpie
I'm sorry the joystick idea didn't pan out. I'm pretty sure you can pair up a Xbox controller to your computer. What may be helpful is if you keep the controller in your lap with your right hand centered on the controller. (you'll want to hover over the area in between the D-pad and the right stick) It will be weird at first, but you'll be able to move, turn, and pick items up fairly easily.
Combat may be an issue when it occurs, unless you sail with a crew. I think a sword or even the Trident of Dark Tides (if you can find one) may be your best bet. Until your hand is healed though you may want to avoid other pirates as best as you can. If you're on a sloop, use a dark color scheme, sail into the wind and take full advantage of the fog bank or the storm when you can.
I hope your arm gets better!