Okay, so I finally got the water wiggler temp to 99.5ºF by upping the set temp of the incubator to 102.5ºF.
I don't think the thermostat probe is out of calibration because a second thermometer held at exactly the same position as the probe reads the same as what's on the display. It just happens to be a full 3ºF cooler at the bottom of the incubator. I didn't get any responses to my last question, but pictures suggest that other users have run it at 99.5ºF and gotten that temp throughout the incubator.
Perhaps the new fan cover keep the heat from circulating enough?