Re: alarm beep?
My Merc '00 200 EFI always provides a short beep when you turn the key on to let you know the alert (alarm) system is working. Beyond this, while running if you get a long steady beep it is an overheat alarm; if it is an intermittent beep, it is a low oil alarm.
You say you recently sunk the engine, if you are getting a continuous beep when the key is first turned on it is either an electrical short (related to the sinking) or it may be an indication of a very low battery, as this has happened to me once.
When you sunk the boat/engine, did you get the engine running fairly soon and heat it up to allow it to dry? Was it sunk in fresh or salt water? If it set up too long, especially while full of salt water, you may very well have some corrosion in your wiring setup which would cause a short.