THANKS for all the replies and info.
For the good of the group- The twin Suzuki DF175s weigh about 474lbs each and put the factory deck scuppers under water. I plan to relocate them and change out the hoses this spring. I have only been out a couple of times but I am very happy with the power and performance. The narrow hull does require active trim tab management.
A few thoughts and/or questions on the matter... how far underwater are the scuppers? Is this with the gas tanks full, halfway, empty? Do you have an auxiliary fuel tank? If you do, do you always have it full? I just have the main tank without an auxiliary fuel tank, but when my 228 Seafarer is 3/4 to all the way full of fuel, the scuppers sit at about the waterline, or maybe even slightly underneath it. I put my boat on a mooring buoy in front of my beach cabin on Whidbey Island here in the Seattle area this summer from mid July until early October. For almost 3 months, I didn't have any issues at all, though I did make sure that the rubber scupper flappers were brand new this year. My thoughts would be this, if you put new rubber scupper flappers on each year, they're supposed to drain the water out but not allow it to come back in. Unless you moor your boat year round, especially in possibly inclement weather, I don't think you should have any issues with water coming back into the boat, even if the scuppers are partially submerged. Or at least I don't think you'd need to go through the process of relocating the scuppers up higher for any reason. You could also try relocating your batteries into the cabin or further forward, which could possibly make it not sit as low? Or even not run a full main fuel tank as well as a full auxiliary tank, if you have one? It looks like a 1995 Yamaha 2 stroke series 200 hp outboard has a dry weight of around 410 lbs per motor. If that's the case and yours are about 65 lbs more per motor x2, then that's about 130 lbs. Marine batteries are oftentimes a bit heavier than regular car batteries and if you've got two or even three batteries in the boat sitting at the stern, then two of three of them at 50+ lbs each could potentially counteract the amount of added weight from upgrading to 4 stroke motors?