It is unlikley that your camera mod will have affected the Bayer Filter. Most mods only involve the blue cast IR filter that stops most of the Ha wavelengths. The Bayer filter is actually bonded to the face of the sensor and is not easily removed. The only way I know of is to polish it off, it cannot be removed with a solvent, it has to be physically removed through abrasives like glass polish. The odds of damaging the fine gold wires on the sensor are high in that situation. JTW has the debayering process posted on their website.
http://www.jtwastronomy.com/tutorials/debayer.html
Perhaps you should read this article by Craig Stark before you think more about it:
http://www.stark-labs.com/craig/reso...yering_API.pdf
I decided against it, but I have a Nikon D70 sensor that I am thinking of debayering for the Cloudy Nights DIY camera project.