I just got back from Japan about 2 weeks ago, it was my first time going, it was awesome you will really enjoy it! I went to Tokyo (Shinagawa, Shinjuku, Mt Fuji etc), Nagoya, Hiroshima, Kyoto, and Osaka. In the Tokyo area, the highlights were the Tokyo tower, Sky Tree, and I really loved the Shinjuku night life. I went out on a Saturday evening and the place was BUZZING with people. Tons of lights, shops, and small restaurants. Had some weird fried kabbobs of pork and liver (not really sure what it was but it was great) with cold sake.
Tokyo Tower was cool, but Sky Tree was much more impressive. There is a small shopping area underneath, and the building is massive. I have seen the Burj Khalifa last year which is the tallest building in the world, and this thing was almost as impressive. Make sure to go close to evening so you can see the view during sunset, and you also get to see the Sky Tree all lit up when you leave.
Mt Fuji was so-so. This time of year you are most likely going to see the base of a mountain with a huge cloud covering most of it.
Nagoya is where Toyota city is located, which is why I went. I took a factory tour of the Tsutsumi assembly plant, it was really neat. They take you on a tour around the inside of the assembly plant. They also have a small museum at the main meeting area for the tour, where they then take you in a bus to the assembly plant. There was an LFA and an FT86 in the museum but don't expect to see a whole lot. Beware if you go here, Toyota city is far from the train station and nobody speaks English in the area, so get all your directions in written Japanese so you can get someone to point you in the right direction. You have to take a train all the way to the end and then a bus from there, we had a hard time and were almost late. Also if you want to do this tour you have to sign up online in advance. Worth it in my opinion.
Also saw the railway museum in Nagoya, was really cool to see the history of Japans train systems from the beginning all the way up to the Shinkansen (bullet trains) and future Maglev trains. Highly recommended. There are also two other Toyota Museums dedicated to the history and older stuff of Toytoa on the other side of town, though I didn't have time to go to either of them. Other than that Nagoya was an industrial, ugly, old and dirty place.
Saw the peace park in Hiroshima where a building directly below the epicenter of "Little Boy" was dropped and the entire city was decimated. The building is in shambles but still stands and is preserved as a remembrance. Very cool to see.
Kyoto had a lot of shrines and temples, nothing too new and different. The Kyoto station was the highlight of Kyoto for me. It is HUGE. Tons of shopping and tons of restaurants. There is even a "Ramen Alley" where I got to have my much desired taste of ramen. Tons of restaurants serving only ramen, it was really good. If you want this research the location because it is impossible to find unless you know where it is in the huge station. No english so choose your ramen at random lol.
Osaka was my second favorite area after Tokyo. Huge modern city. Half the city, and I say that without exaggeration is underground. There is a HUGE underground area in Osaka filled with shopping and food. Ninja Castle was another highlight. Coolest of all was the Umeda observation building in Osaka, it was the biggest highlight of the city. It is a really unique tall building with escalators that cross over from one side to the other with nothing below you at full height. Really great views from there as well. From the lookout, you can see a HUGE Ferris wheel, which I rode, and recommend you do if you are there. It is seriously gigantic and offers a great view of the city as you end up going higher up than most of the buildings. It is about a 10 minute or 15 minute ride in an air conditioned box. Not for the faint of heart but worth sucking it up if you don't like heights lol.
My biggest recommendation is to get specific directions from your hotel front desk every day before you head out. Have them write the directions in Japanese. There are a lot of English speakers at information desks at train stations and such but sometimes you wind up completely lost and nobody can help you as hard as they may try. You shouldn't have to worry much in Tokyo and such but smaller areas have less English speakers. At the very minimum know how to speak and pronounce your destination and they can say yes or no as to whether or not you are getting on the correct train. Most train stations have English and Japanese signs so it is not too difficult.
You mentioned the fish market. Unfortunately I fell sick on the day we were going to the fish market so I didn't get to check it out, though we did drive by it one day when they were closed. You have to go extremely early in the morning but should be quite fun.
Almost all the restaurants you go to will have a display case showcasing all the different food there, so even if you don't speak Japanese you can just point to what you want. The plastic food plates are actually quite comical.
Absolutely without a doubt find a place that sells real Kobe beef. If you are a meat lover, you must. We found some in a hotel restaurant in Osaka. We paid about $75 US for a cut that was maybe 6oz, but man it was the most tender piece of beef I have ever had. Definitely make sure you try this.
Also, if you don't know how to use chopsticks, make sure you learn, because I didn't see a fork the whole time I was there.
That was extremely lengthy but hopefully gives you some insight. I just got back so I am still pretty excited about it, it was a blast, you will have a good time for sure. It is fairly hot there right now, around 85 probably, but we did a lot of walking, just make sure you stay hydrated. For sure post some pics when you get back and let me know if there's anything I can guide you with.