I had pretty much the same problem some time ago. I switched to using my left hand for the mouse, but even that hurt after a while. So I got a touchpad from cirque. They are about 40 bucks for the USB version (I don't recommend the older ps2/serial versions that I used earlier, unless you want to play around with getting the driver correctly installed). Also, I got a Comfort Keyboard (about $300), and I don't use my thumbs for the space bar, I use my index fingers. I found the book Repetitive Strain Injury to be very useful in general (for good posture, input habits and exercises for healing the tendons), though it didn't specifically address this problem.Link:
http://www.amazon.com/gp/product/0471595330.
Now I can use a regular mouse again, but I have meanwhile learned to use a trackpad with either hand, a mouse with either hand, and any weird keyboard
:)
Hope that helps.
BTW: It is amazing how bad touch-typing is for your hands. I completely changed my typing habits, and as a result I don't type fast (while using lots of backspace). I think through what I want to write and then type it slowly but accurately. It has done wonders for my hands.