Before going in on an ECM, have you checked to see if you were down a cylinder or have water in your combustion chambers on one cylinder? In my experience, this doesn't necessarily cause rough running. There may be a little shake at idle, but nothing that would typically alarm me. That water in the intake without water in the cowling anywhere makes me think you have water in the combustion chamber through a bad head gasket or corroded/cracked/warped head. This is an issue I've now seen a couple of times, though I wouldn't expect it since it sounds like you're on freshwater. It can be hard to detect these leaks, and unlike a car engine, you can't just see if your coolant is low since with raw water cooling, you've got unlimited coolant.
It's possible that the water came up the exhaust, but if your exhaust valves are open when the engine shuts down, allowing water into the cylinder from the exhaust, your intake valves were closed when the water entered, preventing water from entering the intake--unless your turn it over after water is already in the cylinder and push the water out the intake on the next stroke.
I would first do a drop test to see if you're totally down a cylinder (and you don't have to really take a ton apart for that, just unplug coils). But because even with water, you can have some combustion sometimes, depending on whether the plug is fouled/how much water, the drop test isn't definitive if you don't see a cylinder down. So if you don't see a cylinder down, I would also do a compression test. When you pull out the plugs, examine them for rust, but again, that's also not definitive. Do the compression test and see if a cylinder is low (it can be as little as 25 lbs lower than the others and leaking, so 175 versus 200). You might also use a borescope through the spark plug hole to see if any of the valves are rusty or there is obvious evidence of water in the cylinder.