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As one of possible options I can recommend you using one of gyration mouses for half an hour or something when your hand start feeling uncomfortable.
I don't think you can use it all the way thus replacing usual mouse since your hand does not last long waiving with this device for an extended period of time ;-) but it's good using it for a change and get your fingers rested a bit.
Sticky me if you need a link to the mouse producer.
Warning! Others may find it kind of cool teesing you while you conduct in front of your PC :-)
I Logitech "Marble Mouse" trackball. I miss the scroll wheel on my mouse, though. Sometimes my thumb gets stiff after a long day.
I also have a Megamouse pad strapped to my chair arm..this has made the biggest difference in eliminating mouse use pain for me. My elbow and wrist used to get sore from extending my arm and resting all my weight on my wrist.