I had RSI in a bad way, and couldn't stop work (long story, but it had a good ending).
The stretches are by far the most important thing. Doing them more often and more painfully than desired is important. Get some squeeze balls and other exercise tools that strengthen the squeezing motion of the hands and fingers (not that this is the RSI problem, but as you work on the other muscles, this will balance that work out). Then, for stretches, place left hand fingers on right hand palm/wrist and vice versa (i.e. palm side to palm side), and then push and hold, so that your wrist bends at least 90 degrees "in the wrong direction". And then push and hold some more. And then some more.
Next, stand up in front of your desk. Place your right palm on the desk, fingers extended. Turn your right hand counter-clockwise as far as you can, so that your fingers are almost pointing back at you. Now, straighten your right elbow (ouch!) and shift your body away from the desk so that you begin stretching your wrist. Do this a bit past "ouch" and hold it there. Now relax, and slightly rotate the hand in either direction, and repeat. And repeat. And repeat.
Do the stretches more often than you want to. Also, learn to avoid the mouse (EVIL MOUSE!) by learning keyboard short-cuts for everything. I settled on the Kinesis Advantage Pro keyboard (I have two of them, i.e. home and office). I've also been trying to learn the KeyMouse, but I don't think that it's a good idea for someone trying to recover from RSI (even if, once learned, it might be a good way to avoid RSI.)
One last stretch: Sitting in your office chair, put hands palm-to-palm, finger-to-finger (as if doing some sort of religious praying) with the fingers pointed straight up. Holding those palms flat together, push the wrists down toward the floor until it begins to hurt, and then push further, and then hold.
Remember to intersperse the stretching exercises with "compression" (ball squeezing etc.) exercises. Good luck