Water thru the scuppers at launch and retrieval is normal for old Aquasports. The deck is designed to be self bailing out the scuppers. Problem is they were close to the water line when these boats were new. Over time like people these boats gain weight with age due to water soaked foam etc. The angle of the boat at launch and retrieval places the scuppers temporarily below the water causing the decks to flood. This is more annoying than it is a danger. The water should not get into the hull unless you have holes in the deck or leaky pie plates. You could plug the scuppers but the easiest thing to do is install a set of ball type scuppers. I prefer the ones made by TH marine since they have a two piece design to allow for easy cleaning. Here is a link to the type of ball scuppers I use:http://www.jamestowndistributors.com/userportal/show_product.do?pid=9138
Regarding your engine fuel issue:If you're getting heavy fuel contamination...yes, the big filter can clog sufficiently to prevent fuel flow.By running a clean aux tank through the big filter...you've isolated your problem to the main tank/ fuel line to the big can filter/water
Had to halt my scupper problem. Having some motor issues. 90 Yamaha c series running ok at idle overheating at high rpms. Changed water pump and thermostat. Suspect pcv or salt deposits. Boat sat for a year and a half. Any ideas