1) Use an alt keyboard layout. Use colemac. It's easier to learn than dvorak and decreases finger travel at the keyboard
2) Stop using a mouse. I used a trackball for a while but it has its own issues. I use a cheap wacom bamboo tablet now. It's far and above more ergonomic than any other device I've used as a pointer.
3) Use a kinesis advantage. Blank keycaps for style points.
4) Use your left hand. I use the wacom bamboo tablet with my left hand (I'm right handed.) This has had amazing results for me personally with the wacom because my left wrist does not bent/turn at all - I move entirely from my elbow primarily because I'm not that dextrous with my left hand.
I did them in that order but I'd recommend swapping the keyboard and mouse first, as they have the biggest bang for the buck in terms of ergonomics. The alt keyboard layout is marginal. Left hand was big for me personally.
All of these items take some time and effort, in particular learning another keyboard layout. And the kinesis also has a relatively steep learning curve relative to other keyboards. Don't do it all at once - it's a multi year journey but hey - no more hand pain! I still use a regular tenkeyless mechanical keyboard and mouse at home in the studio, and obviously carry a laptop for work, but my use of these is fairly infrequent relative to the 40+ hours a week at my desk at work.