Ed, I would guess that unless there's something really drastic calling for a rebuild (flooded cylinders, blown head gasket, etc.) it will take you more time to find out what's wrong with the engine and how to make it right, than to actually do the work it needs.
A reliable auxiliary engine is a wonderful thing to have, I'd suggest getting it in working order (or at least, finding out if that's going to happen short of a rebuild) before taking the boat out. There are many ways to get in trouble on a sailboat if you have no engine and no sailing experience. And a few more even if you have the engine and experience. (G)
An Atomic4 is an exceptionally durable and reliable engine once it has received routine maintenance. There just isn't much to break on them, and aside from the carburetor (ALL carbs need to be rebuilt about every 5 years) and dog simple ignition system (cap, points, rotor, coil, plug wires--it still isn't a lot to replace) the heavy metal parts tend to be so overbuilt and understressed that they are unlikely to fail.
I would suggest initially ignoring the carb rather than taking a chance on compounding your problems, but once you have the engine running smoothly, consider taking a weekend to either do a "major overhaul" of the carb, or swapping it out for a professionally overhauled one. That's a half-day job once you're familiar with it, a weekend if you aren't familiar and have to keep looking at the book, but the nature of carbs is that they DO clog and they WILL go out of adjustment, so a fresh load of fuel, a fresh fuel filter, and a carb overhaul will make your engine much happier. But again--don't make that an added complication right now, if you've got other problems to deal with.
One thing sailing teaches you is patience, like it or not. No wind, no tide, no engine...You're going to have to deal with the "waiting" part of it. Grab your favorite beverage, maybe some tunes, remember "this too shall pass". (G)