Started getting fairly severe RSI about a year ago. It's at a manageable level now, but was really scary there for a while. The things that I credit (this is difficult to measure) as most helpful, in descending importance:
1. See a physical therapist and get a stretching/nerve glide regime from them.
2. Take lots of breaks to do the stretches.
3. Ergonomic keyboard (I'm using a Kinesis Freestyle 2).
4. Use foot pedals for CTRL, shift, and meta. I rigged up a simple 2-pedal Arduino solution for myself. Code here [0]