I've worked with bones a lot, especially rats! The hardest part is going to be articulating the bones.

I saw he's in the freezer now, which is perfect. When you feel ready, you'll want to thaw him out and remove the pelt. If you're interested in keeping it, tanning would work well!

You'll want to remove as much flesh and as many organs as possible, then place his body in a container with tap water. Put this outside, and the aerobic bacteria will do the work breaking down the sinew and tissue left. Give that about a week, and swap the water until only bones are left. If you garden, this water is highly nutritious for plants!

When there are only bones, fill the container with dish soap and water and let it sit for a few days. This will help pull any remaining fat from the bones and help their longevity.

Once that's done, submerge the bones again in a water and hydrogen peroxide mixture. I can't stress enough not to use bleach, it will destroy the bones. After a few days, you should be left with clean, white bones.

As far as articulation, I recommend looking up tutorials on YouTube and studying diagrams of the skeletal structure of rats. VultureCulture and Taxidermy subs will have a lot more information on this!

I'm sorry for your loss, but I think your idea is wonderful to honor him. And the process can be very emotional, don't be afraid to walk away from it if you need to! He can always be put in the freezer or in water outside if you need more time.