From the H-D shop mechanics, and a class on "Winterization" :
Sulpur in fuel creates deposits in the oil. Water in condensate creates sufuric acid. You don't want your engine sitting in sulfuric acid.
Get the engine thoroughly warmed up, drain oil. Let the pan drain thoroughly. New oil. New filter. Crank it up and go for a ride -- get the engine up to running temps.
Cold engine just moves the condensate around. Hot engine evaporates the moisture and drives it off.
Worse thing you can do is start your bike, crank it over a minute or two and then shut it off. This just moves the sludge into your engine -- along with the acid.
New battery for the H-D runs about $175 these days. Battery tender can be had for about $25. Do the math.
Put the Jiffy Stand on an insulated "coaster" -- H-D sells one, but a piece of wood, floor mat, carpet works too. The stand will ground the battery w/ the floor and discharge it. Crud between battery terminals can create a circuit and discharge the battery. Clean is good mechanics.
Top off the fuel tank, leave no room for condensation. Add a stabilizer specific for H-D. The same reason you want diesel class oil for the bike. H-D dealer has stabilizers / octane booster for the bike. Service Manual warns against using non specific stabilizers.
Wash and wax. Dirt deteriorates paint, corrodes alum, chrome. Of course H-D sells polishes, finishers for chrome and alum.
Don't store the bike around fertilizers, cement, pool chemicals, (your meth lab . . . :redrolf

-- chemicals create corrosive atmospheres.
You can put the bike on blocks to get off the tires. But the tires will round out after storage from about 30 miles of easy riding. They're stable materials, get warmed up and come back together.
The other option besides blocks, is to roll the bike forward and back to move the tires off one spot -- every couple weeks. I purchased a "wheel cleaner" from Harbor Freight, which allows me to rotate the wheels.
Cover is nice. Get one that doesn't trap condensate. Personally, I like to tinker over the winter, have access without a cover. Still, I might look into a cover.
Finally, take the bike off the insurance policy. No point in paying for insurance when you're not riding. Keep the comprehensive in case it gets stolen or the garage catches fire, something falls on the bike.
When the bike is off the insurance rolls, then you're not tempted to take the winterized machine out for a spin because the weather allows. You want clean oil and a topped off fuel tank for storage.
-- This is the word from Certified H-D mechanics. Paradise H-D in Tigard OR, October 15, 2011.