Wooden plugs? 2-part epoxy? If installing a Raritan PHII (not a PHC), the plastic base cover will probably cover up any old holes, providing they are reasonably close to the new mounting holes.
But my favorite method is to remove the existing head, clean the area well, then cover it with a custom-fitted piece of Starboard, teak and holly-faced marine plywood, formica-faced marine plywood, etc., in a matching or contrasting color. You can find a nice molding to cover the front edge laminations of the plywood that would normally "show." But don't put it down with 5200 or other permanent adhesive. Screw it down! By screwing it down, it can be removed if necessary, at a later time. With stainless steel screws and marine-type finish washers, it'll look pretty good. Put the screws about 1" in from the outer edges, so that they won't interfere with where you'll be mounting the head or running your hosing.
After installing your new "floor," set the head in positon and mark and drill where the mounting holes need to go, and where any holes will have to be drilled to run hoses. Then install the head and plumb it up. When all done, caulk the joints where the new floor panel meets the vertical walls with a soft, removable caulk, and you're done. It makes a nice weekend project for a Do-It-Yourselfer, and you end up with a nice, professional-looking job.
Larry, is there any water left in Lake Travis these days? I'd heard that with last year's droughts, there wasn't much water left in the lake. I was there about 10 years ago, to a Summerset Houseboat convention, and there was plenty of water there then.