[VoyT]

We were there last year. I didn't think Rappongi was so bad (more Americanized restaurants), but Shinjuku was pretty strange. Then again, we wandered into an area of Kyoto that was pretty strange, too.

Yes, everyone is very polite. Not sure English is that widespread, but everyone knows and says, "Thank You."
The subway sytem is easy enough, but I'd have someone walk you through it. If you take cabs, remember that not all cabbies speak English. A tip: go to the hotel's front desk and grab a few business cards that have the hotel's name in both English and Japanese. In a pinch, you can hand it to the cabbie.
Just about every restaurant has wax reprensentations of its food in the window, along with the price in yen. Some also note that they have a menu in English.
Also, train stations are good places to get food at reasonable prices.
I suggest you check out the food markets in the big department stores ... home of the $75 melons and fruit that looks as if it is on steroids....