I assume that you have not re-powered and so we are talking about an Atomic 4 here? Likely the original, late model?
FWC - so you have anti-freeze circulating thru the water jacket. And you have confirmed that you have water in the cylinders and NOT anti-freeze?
if you KNOW it is water, then only a few entry points for water in the cylinders for a FWC A4.
Have you inspected the exhaust, both wet and hot, from the manifold to the transom?
you mentioned a possible problem with the anti-siphon, yes, that could draw water back to the manifold. But so can an obstruction in the exhaust, as well as breach in the inner wall of the water lift.
before you closed the raw intake, how was your exhaust flow at the transom?
Since you have not received much feedback here on this forum, strongly encourage you to post your issue to the A4 forum at moyermarine.com Tremendous number of helpful A4 owners, much more knowledgeable than me. and when you get everything sorted out, just ask that you circle back here to this thread and update us here on the cause and subsequent resolution of your problem.
C&C 27 Mk I, #45, Vermonstah