Adam, my immediate concern is your gearcase. You mention that orings were replaced, so does that mean someone had the gearcase all apart? Now, you say the gearcase was full of water when you checked it? You need to return the engine to whoever you paid to do this work immediately.
First, refill the gearcase with gear lube to minimize rust damage.

The lower gearscase has several places that can leak. Did the o-ring on the shift rod get replaced? It’s under a brass bushing thathas to be pulled out to replace it. If you have the electric shift this is not a concern, as there is no shift rod. If the propshaft and/or the driveshaft are worn where they rub on the seals, it will leak and you need to replace these shafts. Look carefully at the lower housing for cracks also.
Dave

That idle carb passage that runs from the bottom center of the carb bowl, up the side of the bowl casting can be tough to get hardened deposits out of.
Soak, and/or keep spraying carb cleaner down the hole in the side with the small tube that comes with the cleaner spray can. It took about a full minute of spray to get all the crud out of the last Big Twin I revived.
Dave