There is the bus route that goes to Shinjuku Station West Gate until 12 midnight. Can you not take this bus? Assuming you are taking the SFO-HND by JL, the immigration clearance and the baggage pickup will be completed in 40 mins or less after deplaning , so you should be able to catch the bus leaving at 11:10, 11:20, 11:30, and midnight. You will have to walk a little bit from the west exit to your hotel but it's not too bad.
http://www.limousinebus.co.jp/en/pla...es/index/4/214

For the JR East Pass, I suggest you do that on the following day as you won't be using it on the day of your arrival and ticket offices may be closed by the time you get to Shinjuku station anyway. There is the ticket office right across the street from your hotel and starbucks so you go there in the morning to get your pass and enjoy american coffee if you like

I don't think you need to learn any Japanese as we are willing to help if you ask for one even though our English speaking abilities can be really sucky. It's interesting that you mentioned Sake. hope you enjoy seafood or anything Japanese at least. If you don't, I think food that goes great with Sake can be limited. You don't have to like seafood but if you like it, that's better is what I am saying. I know three great sake places after my personal research. One sake standing bar near the homo district. The one traditional sake bar near Harajuku. The other one is in the biz district with the self electronic ordering system. If you like, I can take you to one of them. You can private message me.

If you go to a Japanese book store, there is the men's fashion magazine "Pen" and their special edition called "Pen+ Real Tokyo Guide 2012" is pretty cool as it has real information that you cannot find in the guidebooks. They are written both in English and Japanese. It's not exactly "gay" or anything but still good Just my 2 yen (cents)

Good day!