in my first year at music college i developed RSI, my hands were in so much pain, couldnt lift a cup of tea or hold a pencil.
didn't play for about 6 months also had to take anti-inflamatory drugs and massage my hands, my doctor told me i wasnt anywhere near the first musician he'd seen with RSI, but I kept studying and playing as absolute little as possible on the guitar just learning arpeggios and scales, i used gauge 8 strings tuned to Eb.. but really went to town on composition, ear training & sight reading.
after leaving it enough time to heal i developed a good warm up before playing, similar to john petrucci's method and i mean EVERY time i play i warm up.. i've not had a problem in 2 years and i use Gauge 10's in E standard now, and i don't shred as much but i can still do it.