The 30th of December to the 3rd or 4th of January is a major holiday here, and a lot of people go back to their hometowns, so trains, buses and planes are packed (the trains actually run up to 130% capacity with people standing in the aisles for hours. A lot of Japanese-owned businesses and restaurants are closed, and the temples are all packed, with the more famous ones having a 2-3 hour line to get in sometimes. Roppongi will have a lot going on, but... lately the police have had "gaijin emphasis patrols" where they take random foreigners that are leaving the bars and take them to the station for a piss test. I can't emphasize enough that you don't want this to happen, as they can hold you for 21 days with no charges, no contact, no lawyer, no translator. The mayor of Tokyo blames all the drugs and drunken behavior on foreigners. A pop star was recently charged with possession when they found .005 grams of "stimulants" in her apartment. They even charged her with using because she admitted she did something while on a remote island to watch the eclipse (they have no evidence or proof of any kind, only her confession). I only tell you this so you're aware of what could happen in Roppongi (The American Embassy had a warning for Americans to stay away). If you want short lines and easy travel, I would recommend a different time frame, even a week earlier or later makes a world of difference.
On a lighter note, if Matt was stationed here, he probably knows a lot of the ins-and outs. The hot springs are amazing, and he probably knows the ones that take people with tattoos, if that's an issue. Make sure you go to Shibuya and Harajuku for shopping, Ueno Park for the national museum and galleries. Absolutely check out Akihabara on a weekend afternoon and go to a "Maid" cafe. If you go to Kyoto, it's cold as hell that time of year, but so worth it. Also, the first sumo tournament of the year is in Tokyo starting the second week of January, lasting two weeks.
The Lonely Planet guide has been very reliable for me as to places to stay and see in different areas, as well as local festivals. Let us know as your plans solidify, we can check local sources for things to do. I'm in the south of Japan, if you guys happen to get this far, I'll happily buy you a drink!
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