Sounds like "mouse hand" aka RSI / CTS !
Some suggestions:
1. Learn keyboard short cuts, to reduce dependence on reaching for the mouse.
2. Try trackball / different size mouse / tablet. I have a novel (i.e. haven't seen it elsewhere solution) I use a Logitech trackball with the right hand and a USB wheel mouse with the LED window tapped up with the left hand. That way, I'm not making fine motor movements with the right hand whilst clicking etc - which I do with the left hand. Found that taping up the window on the bottom avoided getting interfering mouse movements.
3. Check your posture, table height, screen position. In my experience most chairs are too low, especially if you are 6' or over. Many notebook keyboards are too cramped if you have largish fingers for extended typing. Get a full size high quality keyboard for the bulk work.
4. Take breaks :-)