posted 01-17-2004 12:25 PM ET (US)
Modern outboard motors are made with mounting holes that conform to a standard layout. If you have a transom that has been drilled with a non-standard hole layout, I recommend you fill the old holes and drill new holes in compliance with the standard engine mounting template that was provided with your new motor.I don't understand your description of the mounting arrangement of the older engine. It was common for older outboards to be fastened to the transom using a clamp arrangement in contrast to the now-standard technique of through bolting the engine to the transom.
To repair the old holes, you should use plywood filler plugs, not dowel rods, tapped into the existing holes and perhaps glued in place, too. The plug length should allow room on each side for filling in the hole with some thickened resin/mat mixture. Finish off the holes with a top coat of color-matched gel coat.
On some older Boston Whaler hulls the transom was designed for a 15-inch shaft length motor. This makes installation of modern 20-inch shaft engines more difficult. If you have this additional problem you should research for articles discussing this; there have been a number of them that will provide you with good advice.