been using dvorak for > 15 years. switched because of pain from coding 12-14+ days at startups. also used a kinesis advantage for ~10 years. am now on a topre realforce, which i very much prefer over the kinesis, and have been for 6 months without the pain returning. so, half-splitting the problem, i don't think it's the keyboard.

worth mentioning: i can't imagine typing in qwerty now. it just doesn't have that buttery flow that dvorak does. i'm quantitatively 20% faster at typing now as well.

however, i've come to the conclusion that of all the changes i made at the time, buying a good chair and desk made the biggest impact, because in the process of doing so i did enough research to realize i had to correct my body position.

at the time i had an anthro fit console cart and a humanscale freedom chair. these two were the perfect combination.

there's a collection of pretty good information here: http://www.hermanmiller.com/research/topics/ergonomics.html

i am now using an aeron chair (not because of the herman miller guide above) with an anthro 60" adjusta unit for my computer workstation and a 48" standard unit as a return desk. the main reason i switched to an aeron is that the freedom chair wasn't good for my needs, which changed (i have a fairly high metabolism and stay very warm during the day, so the cooling the aeron offered was very welcome).

i was using the freedom chair with a fit standard cart for a while, and the pain returned. immediately purchased a desk with a height adjustable keyboard tray that would allow me to have my keyboard in such a way that my shoulders were relaxed and my elbows were neutral. pain went away immediately.

Edit: sorry for the edits, i've had a little bit of wine.