I would definitely get some Seafoam in the tank and take it for a good ride (at least 20 miles or so) to make sure the Seafoam gets down into the carb and sits there all Winter. The first year I didn't do this, my carb got clogged up with ethanol gunk. In the 4 Winters since, I've used Seafoam and it always fires right up in the Spring and I've never had to go back into the carb.
I store mine in a heated area, so don't worry about whether my tank is topped off. If I stored it in an unheated area where condensation in the tank would be an issue, I would make sure the tank was completely full. I don't think it matters much whether you put the Seafoam in before the gas or after. It should mix in the tank.
I probably waste a lot of Seafoam as I'm sure I add more than is called for. This time of year, when I never know if a ride will be my last, I usually put in about 1/6 of a can with every fillup so if I suddenly stop riding, it's already in there.
I guess it depends on where the bike is, but I consider leaving a Battery Tender hooked up all Winter an unnecessary fire hazard. I just hook mine up about once a month or so until the charge is topped off, then disconnect it.
I've heard it recommended to not start the bike and just let it idle for a short period since that introduces moisture into the engine and oil that's not completely burned off if the engine doesn't run at operating temperatures for awhile. That theory makes sense to me.
I've never thought about tires, but mine's usually up on blocks. I really don't think it would cause any harm to the tires if they sat in one spot for 3-4 months, but it would probably be a good idea to check the pressures regularly and keep them aired up since most tires slowly leak air. Since you're not actually going to be riding on them, I'd take them up to max pressure each time I checked and aired them up.
Guess if you have the space to roll it, it wouldn't hurt. I don't have a center stand and just use a couple of concrete blocks and some pieces of scrap wood to "lift" mine.
If you're going to store it in an unheated area, make sure you get a good coat of something on the chain so the side plates won't rust up and make sure you test your coolant mixture.