Well you do have a long winter ahead of you so here is what I would do.
1. Right on the throw away oil and filter. Change it right now for it's hibernation and then only ride it for a bit in the spring before changing it out again. I wouldn't bother with a reusable air filter. I've got over 70k on my main bikes paper one and it hasn't needed changing yet. (K1200) Check for any metal in the oil as well, you don't know what's it's been treated like.
2.Tires, Highly subjective but yes, get those swapped out. Not worth taking a chance on them. I like Pilot Road 2 and 3 but the choice is up to you there.
3.Bars, again, highly subjective but if you liked stock on your last B12 why not go back to that.
4.Levers, Knock off ones work just fine for a street bike for me. On a dirt bike when you are crashing more often, get the good stuff, but if you go down on the street, levers breaking are probably going to be the least of your worries.
5. Chain and Sprockets, Check the condition of what's on there first. Any stiff links? Sprockets hooking? If everything looks good, just give it an adjustment and go. However if you plan on keeping this, I would go for a new set. I personally like JT steel sprockets and DID X ring chains. They have lasted forever on my chain drive bikes with minimal care.
6.Suspension, Stick with stock (as long as the fork seals are good and the shock isn't blown out) and ride it for a few K to see if it has any shortcomings.
7.Fairing and Windshield, I would try to repair what you have or find a replacement. Call me a wimp but I don't like riding much below 45 degrees without a windshield. And in your area of the country there is a lot of year where temps are around that mark.
8.I think the B12 seat is one of the best ones out there. Leave it alone if it suits ya.
I would take all the bodywork, tank, seat etc off and give it a really good cleaning first of all. That will let your eyes hit every inch of that bike and see if anything looks off.
Good luck and enjoy your B12!