Why can't you fog a bike when it is running? Just spray the oil in the intake at idle till she chokes out or nearly chokes out.

 

I like to fog the cylinders by removing the plugs and spraying it right in, or just add about a t-spoon in each cyl. Then with the plugs out and the trans in 5th or 6th gear, either push it a few feet or just rotate the rear tire just enough to move the pistons through thecyl bore once or twice. You can use a variety of oil's for this, but there are products made specifically for the job.

WD40 is a solvent, and will remove the oil from the cyl walls....as you already found out.
When winterizing a bike that I am 100% sure I will not be using until the Spring, I also like to remove the battery and put it on my charging shelf (I have a small set of shelf's lined with plastic, and a good amount of baking soda at hand with a smart charger with multiple leads on it so I can charge 6 batteries at once if I need to), and run a trickle charge on it once a week or so.

There is also a bunch of other stuff you could do like drain ALL the fuel from the tank and lines.....or just add the proper amount of Sta-Bil to fuel tank. I think draining is a much better method though.....and so on and so on.
I am sure if you search "winterizing motorcycles" you could come up with a boat load ofquality info. It all depends on how long you plan onnot running the bike, andthe level of humidity and cold where the bike will be stored.