I think you have narrowed it down pretty well to the exhaust logs. I'm not familiar with those, we dealt more with conventional Mercruiser, Volvo, etc cast iron manifolds and risers. You may be able to have those pressure tested to see if there are cracks that are allowing water to get into places it shouldn't be. Sometimes these cracks open up when the boat warms up. You might be able to pull them off and look down the exhaust ports on the logs and see if you can see signs of water coming in there (rust trails usually)

The fact that you overheated the boat so bad could have contributed to them cracking. All manifolds have a certain life expectancy anyway........running in fresh water vs salt water helps a lot, but still they will wear out in time.

Lots of the Berkley powered boats ran big block Fords and Olds, it seems. I looked at buying one years ago that had a 460 in it too.

Don