I had the same issue when I replaced the inspection hatch covers on my '79 HC-18 this passed spring. The fastener holes did not line up. I looked like the hole circle was slightly smaller on the original cover. I chose to rotate the new hatch and drill new holes; centered between the original holes. I filled the original holes with epoxy filler before installing the new hatch. This strengthens the surrounding fiberglass and seals edges from moisture. The new screw-on cover hatches don’t have the strain on them that the original pull-off rope hatches did so that should be fine. Make sure you have a good clean sealing surface and caulk the hatch flange with a good marine adhesive caulk or RTV. I used 3M 5200 Polyurethane Adhesive/Sealant. A good set on instructions for installing a NEW deck port is located at
http://www.thebeachcats.com/modules.php?op=modload&name=News&file=article&sid=29&mode=thread&order=0&thold=0 This includes locating and cutting a new hole, which is more then you need, but the information about mounting, sealing and drilling the holes for the deck cover flange is very thorough. Good Luck.