I'm using XXXguitars super mega normal mapping shader, and apparentley the specularity can be controlled using the alpha channel of the normal map. Does anyone know how to apply a specular map to the alpha channel of the normal map, either using GIMP or photoshop elements.

Any image editor that allows you to edit the alpha channel will work. I use the GIMP, myself. Save your file image as a 32bit TGA file...

with GIMP, you can do this:
[menu]Layers -> Add alpha channel
[layers tab]Right click -> add mask -> alpha channel

then drag your spec map into the white box to the right of the image thumbnail (or something like that).

Hopefully someone that knows more about GIMP can give you better advice