Ok - Back in NC and at a keyboard again.
First, the question on the fish market: It's mostly still referred to as the Tsukiji (Ski-Gee) market, though it has moved to Toyosu. In the early morning (~ 5am) its a live auction of fresh fish, most popular for the Tuna. After that it is pretty dead, but the area around it has plenty of stands to buy some fresh sushi; probably as fresh as you'll come across.
Your question about cash - you need it. The situation has improved greatly in the past 5 years, but you will randomly find a burger restaurant or Korean BBQ that for sure seems like they would take cards, but don't. I generally walk around with ~5,000Y just to be safe (in the US i rarely carry any) but often I don't have to use it. The places that do take cards will take AMEX.
Transportation - There will be an Airport Limosine (brand name - Orange logo) bus that goes directly to your hotel. that will be the easiest to get there. Once you are there, I recommend the taking the train everywhere. Taxi's are expensive. Don't be afraid to mess it up; if you get on the wrong train you can get off and go back the other way for no cost. Get a SUICA card from the machine at the train station (you will need cash to do this). The card itself cost 500Y, then you just load up yen on it and use it as a debit card to ride the train - its an RF thing that you just touch onto the gate. As a visitor you can also get a JR unlimited rail pass for a week or a weekend that is pretty cheap, but that generally has to be done in advance. To navigate the train system, download the app "Hyperdia" to your phone. it will tell you the train times and transfers to where you want to go.
And that dovetails with connectivity - I find the best method is a global WIFI access point. They can be rented from the Softbank kiosk in the arrivals lobby in NRT. Its like 800Y per day for unlimited connectivity and will cover your computer and phone unlike getting a SIM card, then i just enable calling over WIFI on my phone.
More on attractions:
There is a place that you can dress up like a Mario-Kart character and drive around the city. Last i knew it was called Mari-Kart, but i think they were in the process of being sued by Nintendo; hah. I've always wanted to do this, but it's never worked out. You need a translated drivers license before you go (can be had from an AAA)
The Akihabara area is fun to see. It's video game centric with people dressed up on the streets as characters. Everything closes up earlier than you would think though, if you have time I'd take a walk through the area before 7 to experience it.
Sky Tree is a great view, but the lines can be hella long. If you have free time on a week day its quite a bit better.
The zoo in Ueno has Pandas if you are into that type of thing. There is a panda cub there now, so its likely to be busier than usual.
If you want to go out and party, the Roppongi area is where you want to go.
Skip out on Shibuya crossing and Tokyo tower; they often recommended by travel sites but are not worth the effort. The Imperial Palace and Gardens are cool to see, but take a bunch of time.
Any other questions - Just ask.
(I need to find a vendor willing to take me there to do factory tours....yeah...that's the ticket! Mitsubishi, Fujitsu......etc) 
