Still trying to solve problems with white areas

In an effort to insure the problematic white areas aren't caused by stray light from the built in LED light sources, I removed the little panel which contains all the lights from the sensor array. Much to my relief, the scanning back still functioned using VueScan.
Prior to this, I installed Ubuntu Linux on a partion of my hard drive. I used the open source SANE driver to drive the scanner in hopes that the white areas wouldn't be there. They were still there.
I ordered a set of LEE 3" primary color filters a few days ago. Kit includes a Red, Green, and Blue filter that are very restrictive so that they only allow in their respective set of wavelengths. This will allow me to create a full color image by taking three seperate shots through each of the color filters and then blending the images digitally on the computer. Of course, time will have passed between each shot, so many artifacts will occur. I am very excited about how this will look. Furthermore, since the sensor is sensitive to infrared light, that will affect things as well. Look forward to seeing what I get.