While you found the 4 plugs and drained those, you also have to remove the bottom end of the large hose that connects the circulating pump to the thermostat housing, that pump holds a lot of water and it won't drain unless you disconnect that hose. The 5th plug they are referring to is on the front edge of the intake manifold, it may be hiding behind one of the cooling hoses, its probably a square plug. This was a change from the older pre Vortec engines like mine to the Vortec, on the Vortec this area can hold water and can cause cracks.
As long as your exhaust manifolds don't leak internally you can't get get AF in the cyls from filling them, it will run out the exhaust reliefs under the transom mount. The exhaust gas and water passages are separate they only combine at the outlet of the elbow, which is under the rubber exhaust hose, but it won't back up into the engine that way. The only way that could happen is if the manifold or elbow has a crack or rusted through area, or if the gasket between the manifold & the elbow leaks (two piece wet joint style).
BTW, I'd think about converting the one piece manifolds to the better 2 piece style, casting problems with them have resulted in thin wall thickness and cracking and that can ruin engines. THAT problem can for sure put water into a cyl. Barr Marine makes a nice conversion kit. Not cheap but if you are keeping the boat, I'd get rid of those. Merc discontinued them for that reason, could not get consistent wall thickness using the casting method they had. Bad exhaust manifolds are a top cause of inboard engine failures. Here in salt water we are used to replacing them, every 5-7 years due to corrosion.
Here's a pic of that 5th plug.
Also if you have a P/S cooler behind or next to the engine, I'd put the outdrive down, then disconnect your raw water intake hose at the thermostat housing. Hold it down to drain it, then hold it up and fill the hose with -100 marine AF till it runs out the outdrive water itakes. That will push water out of the PS cooler and hoses that go through the transom mount.