Sam,
You’ve got a long road ahead of you to get that boat ready to take south. First advice in regard to your posts, PM, and email is to learn to properly assemble information and ask questions. You’ll find people here very generous with their time and knowledge but not if you waste their time. Full information is less time wasting that questions like, “Engine has water in it. Could it be the water pump?”
Even the seemingly inconsequential can be significant. You mention “Chris”. Someone asks if it is Chris Oliver and gives a good report. You tell me in PM that he was from Portside Marine. I Google “Chris Oliver Portside Marine” and find out that, yes, it is him and they are a Yanmar dealer. I now know that you are probably getting excellent advice but I had to take time to figure that out. I could have spent it scanning the diagram of the pump from the engine manual and sending it to you.
You weren’t clear in your first post whether the water was in the cylinders or the crankcase. That’s wasted effort in which you could have gotten more useful information here. There’s a nice and well informed run down above on what to do if your engine is frozen but it evidently isn’t.
You say Chris Oliver says you need a new waterpump. I’m not sure after the way this has gone that’s what he actually said. Are you sure he didn’t say, “New impeller and seals”? Did you ask why you need a new one? Is the casing cracked? Is the inside worn to where a rebuild won’t work? Does he just figure bolting a new $600 item (that he can probably sell you) will be easier for someone of your experience than replacing seals? Maybe he knows that you can’t get the seals anymore without buying a whole pump or that the labor of replacing seals will be more than a new pump.
The devil is in the details on these things. I know it can be overwhelming but you’ll be facing innumerable things like this before you are down south watching the sunset and learning how to handle and process the information necessary to get the answers you need is the first step.
Some random hints:
Water pump impeller should be replaced every year and old one(s) kept for spares.
The pump isn’t exactly as shown in the manual.
The back plate is a flat piece of metal. Mine wore to the point where the pump wouldn’t prime. I removed the paint from the other side with paint remover, polished it up a bit and it works fine turned over. When I buy a new one, I’ll immediately remove the paint so the other side can be a spare.
I replaced the screws on my pump cover with s.s. metric screws from a hardware store that had hex socket heads. I bought them over length and put wing nuts on them. I can now remove my pump cover by hand. Best to have a hex wrench to replace it but, if I drop the wrench in the bilge while drifting towards shore while replacing an impeller, I can turn the screws in by hand and put final tension on with the wing nuts. The wing nut and machine screw combination is also easier to hang on to and easier to fish out of the bilge if I do drop one.
Replace every screw you can with hex socket heads. Much easier to replace in tight spaces while contorted as they fit snugly on the hex wrench.
Be sure you find all three zinc anodes on this engine and replace them. Put a new thermostat in now.
There is no practical way to drain the oil through the plug on this boat. You have to get a small bronze hand pump and pump it out through the dipstick while the oil is hot after running the engine. It’s hard work. One gallon of oil is just the right amount. I use Rotella 15 W 40. If you are not replacing the filter, which I do about every second change since I change often, leave about an inch of oil in the jug. Too much oil will ruin your engine faster than too little if the moving parts make it foam. This engine is installed at an angle beyond the Yanmar recommendation. It doesn’t seem to have caused problems but you can’t put as much oil in as the manual says. Keep the level exactly at the top of the dipstick hash marks.
Take off the whole hand starting apparatus. You’ll never be able to hand start this engine in an emergency and it will make maintenance access to things like the engine mounted filter much easier.