This.
My mom was having wrist trouble with a conventional mouse, and from using her PC for just a few seconds, I could see how uncomfortable a regular mouse would be. This Evoluent thing was great. It's a bit more difficult to control than a standard mouse, but it doesn't take long to get used to, and is much more comfortable and natural.
I've got a chair with armrests, so my elbow is away from my body, putting my wrist at the proper angle for use with a normal mouse, thus no need for the Evoluent.
Neck - check the monitor level versus her chair.
What kind of monitor does she have? If it's a CRT, set the refresh rate to at least 75Hz, or preferably as high as the monitor will support. 60Hz can cause eyestrain, which might manifest itself as some kind of headache. I find flickering from CRTs set to <75Hz (or some old fluorescent tubes) to cause symptoms similar to motion sickness.