You're staying very near where I was, so, in the immediate vicinity of your hotel there are a couple of decent (chain) restaurants.
Itamae Sushi - part of a large worldwide chain but a good, cheap place and a good intro into sushi/sashimi.
Can't remember name, Okonomiyaki restaurant in the same complex.
also had a great meal at this place, which is nearby - Onegiya Shinjuku ten, Shinjuku - Shinjuku - Restaurant Reviews, Phone Number & Photos - TripAdvisor
If you're not planning on leaving tokyo, then don't get a JR pass..... local travel is quite cheap. If you're wanting to use the shinkansen to travel the country, do get a JR pass.
I don't know if it will cover you on the maglev train, that wasn't open when I went to japan.
Reckon spending a week in Tokyo, then a week outside Tokyo (Kyoto and Nara for a start) would be a better use of your time, There is more of traditional Japan in Kyoto and Nara than Tokyo (personally I would rate them higher than Tokyo and think you are missing a trick by not going there) . Takayama would also be a great couple of days, as it has some very traditional type streets
I appreciate your advice, we will be having day trips outside of Tokyo for sure (Kamakura been one), But there is alot of places we want to go and see in Tokyo (hence Tokyo as a base) and we will happily fill in the time .