If you are making a presentation piece, I would find another piece of wood. Otherwise, I would leave worm holes, bark inclusions, and knots as they are. If necessary, I would use some thin CA to stabilize wood that might come out. Otherwise, I would do nothing until the gun was finished and then fill the holes with black wax. I had a large bark inclusion on the forearm of my chunk gun and none of your ever saw it. At least, none of you ever mentioned seeing it. I waited and waited, and finally had to bring it to your attention. I treated it just as I said above.