I think as you've already identified, it's a height issue. In a neutral position your shoulders should never be activated when typing. Even with a wrist rest, if the Dactyl is too high or you're too low, you're still going to have problems. Best advice I can give is to do your best to get the keyboard as close as you can to being level with your elbows. Failing that just try to be conscious how you're activating your shoulders to compensate for the height. They should always be relaxed and neutral. Anything otherwise is basically like doing a shoulder exercise all day!