I have a 2005 Johnson 15hp with the same general concept as yours. I tend to go way overboard and may be in the same situation as you soon. My way takes longer but I try to do everything the right way.
1) First and foremost, at the very least, flush the motor with fresh water if not a "Salt Away" flush kit which I believe every duck hunter should have for their rig.
2) Run the motor with a high quality 93 octane fuel mixed with good quality 2 stroke oil from a gas station that has a high turnover (busy highway gas stations, higher turnover, better gas)
3) Be sure that above fuel has a healthy dose of Stabil-Marine and a ring-free (Yamaha and Startron are good brands)
4) In the process of running, fog the motor properly with a good spray. You might also consider de-carbing the motor as well with the right spray but do this BEFORE fogging.
5) Run the carb out of fuel (only do this for long term storage as starving the cylinders can cause small wear each time)
6) Remove the spark plugs and give a quick shot of fogger into each cylinder. Replace with new plugs as decarbing and fogging while running will likely have killed your plugs in there (this is normal). Put some dielectric grease on the plug tops before you put the boots back on.
7) Once you're done running your motor, do the following:
a) Remove #15 and #16 in this diagram of your carb. This will drain the float bowl. This is so important. Many guys run their OB dry and think that's it. Nope. Bowl still has fuel in it. Put the screw and gasket back on once fuel stops dripping. You can put paper towels around the carb to absorb the fuel.
Diagram
https://www.boats.net/catalog/johnson/outboard-by-year/1989/j15ecec/carburetor
b) Disconnect your lines from the fuel pump and let that drain as well.
c) Press the pin on your fuel connector to drain any and all fuel out of the lines.
d) Put your fuel pump hoses back on.
8) Drain your lower unit oil and put new in, with new plug gaskets.
9) Take your prop off, clean the shaft, and put new grease on. Re-install. I can't tell you how many guys neglect this and down the line find themselves cutting their prop off because it froze to the shaft. Mine gets removed, regreased, and set with a new pin, every year.
10) Grease all your grease points on the main pivot shaft and all tilt trim.
Now many of you will probably ask, why not replace the water pump? Well, it's probably going to get brittle and rot during storage. You'll need to make a note to yourself to replace it with a new kit when it comes out of storage and put back to use. With all that being said, I don't see why you wouldn't be able to just replace the water pump and get off to the races when the motor is recommissioned.
This is going to be my procedure in the foreseeable future. I am upgrading to a 25hp on my Duck Invader but would like to keep the Johnson 15hp for a sneakbox and/or my kids boat down the line.