Hi Ben,
I found that sanding did not help the discoloring of the wood. I have since tried to avoid use of any epoxy filler. I now fill with small pieces of wood the same color as the surrounding area. All the small gaps (1/16" and less) I don't fill at all and take care of it during the seal coat. All the tiny gaps left over fill just fine during the glassing stage. BTW sanding after the seal coat down to the wood causes discoloration as well.