Oh, you'll have a great time in Tokyo! It's good to see more Aussies going to Japan, I think maybe prices/language scared people off but when I was there in October there were heaps of Aussies - the downside of Jetstar flying there is the tons of bogan school groups we encountered!
You'll still find yourself standing out like a sore thumb though - being stared at is par for the course.
I used to live in Ebina which you are REALLY bored, is an hour to the west of Tokyo on the Odakyu line, but there's not a lot there so I wouldn't recommend it. Most of my experience is with the Kanto area, although if you have a little more time getting out and about is well worthwhile.
To give you an overview of what can be done in 5 days, I'll tell what we did.
I took my sister in October for her first Japan trip, and we flew a red-eye SIN-KIX (Kansai Int'l, Osaka) and then converted our JR passes to get the airport train (Haruka) to Shin-Osaka, then the bullet train to Hiroshima. In the evening we visited the Peace Park and the A-dome. Next morning it was the A-bomb museum (I've been 4 times and still struggle to deal with it) before checking out and heading to Miyajima for Itsukushijima (the floating Torii gate they like to use on tourism ads). The JR stations all have coin lockers and thus you can store your baggage there while sightseeing. Alternatively, takyuubin companies can sent your bag from hotel to hotel so you don't have to worry about them at all. I can't recall the cost exactly, but I think it was about $30.
In the afternoon we got the shinkansen (bullet train) through to Kyoto. Normally I would recommend a stop at Himeji but the castle is under repair. Muchos scaffolding, much like most of Europe when I visit...
In Kyoto it's easy to get temple fatigue. I would recommend Kiyomizu-dera (especially for anyone travelling in Oct/Nov when the leaves are going red) and Kinkaku-ji (the golden temple). I also like to take people to Nijo-jo castle - less of a beautiful multistorey castle like Himeji, but still interesting to look around the buildings and the grounds.
Visiting the Daibutsu (big Buddha) at Nara is interesting, however they were renovating bits of the pavilion in October which restricted things somewhat. The daibutsu at Kamakura, a short trip out of Tokyo, is a good second choice.
We then spent the final 2 days in Tokyo, where trips to Shinjuku (Metropolitan Govt Building for sightseeing, as well as shopping and the chance to visit the busiest station in the world), Ginza and Meguro were in order. Meguro?? Yes, some of us have interesting hobbies and Meguro contains a tiny free museum called the Meguro Parasitological museum. If you've ever wanted to see an 8m tapeworm preserved, now's your chance! I realise this may be a niche interest....
If you stay entirely in Tokyo, I would recommend spending a day in Kamakura/ Yokohama, and a separate day trip to Fuji/Hakone. Kamakura is a former capital and has more of the old feel that is harder to find in Tokyo. Yokohama had the 2 biggest department stores in the world, although I think they have lost their titles now.
For days in Tokyo itself, I would suggest lazy days over the weekend in Harajuku people watching (google cosplay and learn about the oddness you may see), best on Saturdays I think, and Ginza on sundays when the road is shut off for pedestrian use while shopping.
As for the fish market, I don't see the attraction really (Disclaimer: not a fan of fish, can't stand the smell!) but be warned there are restrictions now. The market gets closed to tourists at busy times and also there is a 140-person limit, first in best dressed. See www (dot) japan-guide (dot)com/e/e3021 (sorry it won't let me post a link!) for more details.
Can't say much for accomodation, mostly stayed at budget places as a tourist. There are hotels for all budgets, and it really depends on if you want luxury or just somewhere to crash for the night, and if you want something you are familiar with like a western brand, or if you want to try something new (traditional ryokan).
Finally, useful tools for getting around:
Hyperdia (dot) com (can't auto-link, sorry!)
Tells you which train, where, how much etc.
I think google maps is now incorporating a similar feature including times, routes and costs into Japan searches as well.
And if you don't speak any Japanese, carry the business card of the hotel with you to ensure you get back to the right place in a taxi - they often have maps as Japan doesn't use street names or numbers the way we do so finding places can be hard.
Most train stations have a "police box" near a main exit, and these chaps are good at providing local maps and directions, although their English isn't usually brilliant.
Last thing - Tokyo has the most Michelin starred restaurants in the world now, I believe. Mainly French and Japanese cooking, but assorted others too I think. Either google or contact hotel to see if they can tee up something special for your wife's birthday
Sorry to yammer on, any more questions let me know!
