If you had water in every single cylinder (and a lot of it) then my bet would be exhaust manifolds as well. If you had noticed water dripping out of the ports when you removed them to pull the heads, that would have been a big clue. Failed riser gaskets can do the same thing, but usually wont allow gross amounts of water in very quickly (thus hydrolocking the motor).
I would pull the exhaust manifolds and pressure test them. Both would have to be junk for you to get water in both banks- but Ive seen it happen due to an overheat. I have seen intake manifolds crack from the same overheat, and that will exacerbate the water in the oil symptom. It sounds like the boat sustained some damage prior to you getting it... I'd consider pulling the intake and looking for evidence of water intrusion in the valley while you have it apart.
How long has it been since the water showed up? If its been more than a few days, theres a chance your fresh heads may be all rusted up in the area of the exhaust valve seats. Dry it out ASAP and compression test.