Not tearing into this just yet. Need to clear a work area and get access to boat. I did find plenty of YouTube videos on sealing difficulties with Vortec heads. I looked around on eBay to see what pictures I could find of some used Merc intakes. Seems many of the used ones are rusty. Picture shows a lot of rust around #1 and I suspect my project intake is same or worse as it is an 04 salty. There is a good distance from water passage to #1 but I can now see how this could be a very likely source of the water injestion. We will still very closely inspect the exhaust manifold again or just replace them with some new aftermarket for piece of mind. I keep thinking back to the original first fail day symptom. Complaint was rough running at end of day while putting on trailer. Once home and spark plug pulled a good amount of water ran OUT of #1. No way was that much water present when it was running so I am assuming it leaked into #1 while at rest. This would point more to intake than an exhaust riser.

Pic of used intake from FleaBay, not my intake,or pic of #1 area, just an example of a random intake found on FleaBay. This has me wondering if I do find rust around #1 if I can have the intake resurfaced to clean it up. Would resurfacing (depending of course how much they machine off) cause other difficulties with sealing? I know I am getting the cart in front of the horse here but just trying to get a plan together. I need to get off the keyboard and into the bilge!

That photo of course is the rear end of the intake, with the blind block off for the rear head water port. 1# is about the same.distance from the water passage.

Depending on the depth of any oxidation porosity, a good cleanup and using a large flat sanding board often works.

If eroded where you don't think it will seal, having the intake surfaces machined is no big deal. It just starts to mis-align the intake port match-up a little. That could be offset with a thicker intake gasket.

You can often find used Stainless Marine exhaust manifolds.