Check page 127 in the owner's manual. It tells you the basics of what to do.
http://marine.honda.com/pdf/manuals/00X31ZY96210KIT.pdf
It says to drain the vapor separator, but I would not only drain it, but also flush the fuel system with fresh fuel and drain it again.
If you have a starter repair facility near you, you should probably have the starter taken apart and cleaned soon. Otherwise, it will probably fail in the near future.
Also, while it is out of the motor, make sure all the water is removed from the flywheel section under the starter. If you do not get the water out of there, the salt water will ultimately rust your crankshaft and cause the crankshaft seal to leak. There is also a block plug (that you can not get to without pulling the powerhead) that will rust and cause an oil leak in the future.
The connections are supposed to be water tight, but take them apart and clean them thoroughly.
Theoretically, you should not connect the battery until every connection has been cleaned. Voltage plus salt water (really any water) equals corrosion. Realistically, you will want to crank the engine to get the water out of the cylinders. Be sure to disconnect you safety landyard and disconnect the high pressure fuel pump in the vapor separator while cranking. You do not want spark flying around and do not want the fuel pump to push water up to the injectors. There is water in the vapor separator if your motor went completely under...getting in through the breather vent.
Good luck!
Mike
