I live in Okinawa, and travel to the mainland occasionally (I suppose that's an appropriate term)
I went to Hokkaido last year for the snow festival. I shoot with a 5D3 and during the day my 24-70 II was more than enough, and at night I used my 24mm both indoors and out. I brought a tripod but rarely used it as this was a vacation, not a photo safari.
So, 9 days, flying into Tokyo. I'd try to find the flights going into Haneda and not Narita for starters.
As mentioned, those monkeys only need a day, unless you really have something for monkeys, but IMO there is much better stuff to see around.
But like mentioned, if you're going to see them, you'll want some focal length. You have that covered with the 70-200. I doubt you'll be able to set up a off camera flash close to them... They might grab it and run off with it...
Seriously. Monkey's are azzholes!! Look at these guys on Ishigaki-jima:
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I wouldn't bother bringing a macro, especially as you'll be in the colder regions, in January. Spring/summer? Sure...
The 50 you have will be great for the markets, though you might find it a little tight... I like my 24L...
This is a 3-street wide market right outside Ueno Station
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As far as travel, once you arrive in country, use Skymark or Peach airlines. They fly to all the cities, and cheaply...
There's so much I want to write here, but my mind wanders too much for it. If you would like to chat and discuss things in an easier manner, find me on FB (Ron Wroblewski), my profile pic is me with those monkeys, so I should be easy to find..