I'm thinking "patch". If you remove the holes, the silicone, and everything else in one fell swoop your repair should be faster to make, stronger and less noticeable.

Cut out a piece that is large enough to contain all the boo-boos and replace it with a fresh piece of wood. To make it blend in better, after you cut the hole in the hull, bevel the edges to a 45 degree angle. cut your patch large to be a bit larger than the outer edges of this beveled hole, then bevel the edges of the patch. A sanding disk can do the beveling in a short time. take some time to fit the patch perfectly into the hole. If it is too large it will sit a bit above the hull. If you take off a bit too much it may rest a bit below the level of the hull, but a few pieces of sawdust can be used to shim it into place. The matching beveled edges give you a large glue area, just like a scarf joint. Glue in the patch with thickened epoxy. When the epoxy hardens sand the area smooth (careful that you don't sand through the upper layer of plywood veneer) and reinforce the area with a layer of glass cloth or two on the inside where they won't be noticeable. The glass should overlap the joint edges by at least an inch on each side. If you are mounting rails for your footpegs, you can use them to reinforce the patched area, too.

hope this helps.

Paul G. Jacobson