I developed some RSI symptoms with my mouse hand after doing some intensive data summary work (putting data in static web pages, etc.) for a few days straight. It took several months for everything to feel normal again, even with using a splint, resting occasionally, replacing the mouse with a trackball and using a gel pad, etc. And the pain will still come back if I over do it. Once that nerve is irritated, it takes a long time for it to settle down again.
Nick Petreley once claimed that his four-button mouse caused him to have carpal tunnel (especially using the thumb button as double-click). It never had that effect on me. Everyone is different.
The main thing is to do is figure out what caused the pain to appear in the first place. If it's your posture, then correct it. If it's doing the same mouse motions over and over again, then take breaks and try a different mouse or trackball and try to change your habits. Once it's irritated, it's important to minimize further aggravation - meaning if it hurts, don't do that.
Don't take what you read as gospel. The human body isn't a Chinese block puzzle that only goes together one way. Experiment and see what's most comfortable for you.
The most important things to remember are: 1) Do things in moderation; 2) You're not 16 years old any more. It takes longer to heal up than it used to; 3) Nobody knows your body as well as you do - if it hurts, don't do it no matter what some book says.
HTH.
Cheers,
Scott.