The regular butt breaks have always been our best hedge against discomfort. I set my Timex Tri. watch's countdown/return to a 10 (summer) or 15 (winter) minute cycle that I use to remind me/us to drink and to take a butt break.
However, sore hands usually means poor position/too much weight resting on the hands or bull-horn bars. Traditional fixes: make sure her riding position on the tandem is exactly the same as her single (seat set-back, handlebar to seat rise, seat nose to crank) and if all else fails consider gel gloves or different handlebars that offer more positions.
Just what comes to mind....