find yourself a hardwood plug or Dowel, (Preferably similar color) that fits snuggly into the hole in the shell and glue in there. insert the plug from the inside and leave just enough, (ca. 1/8") of the plug on the outside so you don't have too much to shave off. But be sure to leave enough so that the plug is flush with the shell when you shave it down.
Or, if you don't find a plug of similar color, you can use a beechwood Dowel and touch it up with stain to match...
The inside of the plug you can cut off and file; after 24 hrs go over the plug ends with a fine wood file to clean it up and put a little oil or whatever you like on it. In my opinion, that's too nice of a wood and Bongo to fill with epoxy.
The Bottm Rim hole:
Aluminum or steel, find a matching Rivet or round piece of similar material of a just slightly larger diameter of the hole, (you may have to make the hole very slightly larger to accomodate the diameter of the round piece that you have); cut it to thickness and press it in with a small bar or C-clamp, or you can tap into the hole with a hammer; Or find a piece that is the same size as the hole and glue it with an Epoxy for binding metals. I believe they come in small tubes... Or maybe you know someonewho has some; you don't need more than a thumbnail...
This plug you want to insert from the outside, and you want to leave just a hair of the plug on the surface to be finely filed down and then go over it with #00 steel wool.
I hope that helps. Good luck!