Do a blind test if possible -- hook it up on the sly and see if she still has headaches. The placebo effect can be powerful here, that is, if someone knows they're there, that might cause them to feel the effect.
Does the effect vary depending on where the equipment is placed? RF power fades on the square of the (radial) distance from the antenna. So the difference between standing next to the antenna and having it on the other side of the house should be significant.
Does the effect vary depending on what RF channel you've configured? Resonance effects can cause even very small amounts of power to reinforce themselves and become more interesting amounts of power, and one way to break resonance is to change the frequency.
Does your wife have problems with your microwave oven? Check the inside of the door and the back, there's often a sticker telling you what frequency it runs on. Mine runs on 2450 MHz. I would venture to guess that even with very good shielding, a 1100W transmitter at 2450MHz would end up leaking milliwatts of power... on the same scale as 802.11b's signals, especially considering the r^2 rule.
Do you or your wife have a 1900MHz cell phone? Is there cell coverage in your location? While not the same frequency, 1900MHz has similar properties in many ways to 2400MHz.
I am skeptical that the RF is the cause of your wife's problems, but it is not outside possibility. Treat it as a science problem, though, and see if you can understand better what causes problems and what doesn't. Our understanding of the health effects of RF is still immature and the political nature of the issue doesn't help.
If you really want wireless and don't want to make your wife unhappy, another approach is to shell out for 802.11a gear, which works on the 5200(?) MHz band and should have substantially different RF properties for this purpose.