If you use straight water and don't put any sort of soap in the water, evening boiling water will not affect the color on the bases. I try to not have a lot of water touching the antlers in general. Put the head(s) in an empty pot, then fill to just cover the skull. The only time I have ever had an issue with discoloring the bases, I had 2-3 inches of water touching them and, not thinking straight, threw in some Oxy Clean. Had to stain that whole set of antlers to fix that mistake.
If you do like to use Oxy Clean on your deer, wrap the bases in Seran Wrap first, then secure the seran with the electrical tape.
To remove the glue residue that's on there, I would maybe try a brake cleaner or a Goof-off sort of product and try not to get it on the skull. Just soak a small piece of rag and work in small spots on the back of the antler to begin with to make sure it won't remove the natural color.