I have been a frequent traveler to Japan for 25 years and was in Tokyo two month ago with my wife. I’ll try to offer practical advice for a first time traveler. I think as a first timer a hotel in Shinjuku will be interesting because there’s so much going on in Shinjuku. I just read your have done your booking. I only recommend you get a Suica or Pasmo card at the train station. You can get a refund when you leave.
A decade ago I would visit all the camera shops for Leica stuff but I don’t do that anymore. I recommend MapCamera in Shinjuku and Fujiya in Nakano. The Ginza is worth visiting as well. Buy a photography magazine and the ads for camera shops will have addresses and little maps. If you like vinyl records then Japan is paradise for that.
As for what to see, I highly recommend you look at this link. These trips are worth it. I especially like their package to Kamakura. The electric train ride along the coast from Enoshima to Kamakura is very enjoyable and I have even walked it.
About the Romancecar Limited Express Train Romancec
www.odakyu.jp