Advice on Samurai theme itinerary

My son loves Samurai n all the japanese carton stuff. We are coming to Tokyo on the 29th Nov till 12 Dec. We have 12 nites.

Can some experts recommend how we split our days to see our interest. The kids want to see samurai and anime stuff and we want to see the culture. We are not interested in shopping n Disney.

thanks

1day in Tokyo(Edo Tokyo Museum & Imperial palace)
1day in Nikko(Toshogu shrine and Edo Wonderland)
1day in Matsumoto
at least 1day in Kyoto
1day side trip to Himeji castle
1day side trip to Hikone castle
1day side trip to Iga-Ueno(Ninja city)

These are the must!

Kanazawa has a Samurai district with one of the houses, Nomura House, open to the public. It has Samurai armour on display.
Its a long way to go just for that though: Kanazawa has loads of other interesting things: see the link on this site.
The national Museum in Ueno Park has a lot of Samurai items on display: armour, swords etc
Himeji castle is currently under restoration
To see Himeji, Hikone and Matsumoto you will spend a lot of time on trains: kids may be bored with too much travel: maybe chose one.
Osaka Castle is easily accessible, but a concrete reconstruction: has some display

Samurai and Ninja theme sites in Honshu:

Iga-ryu Ninja Museum, Iga-Ueno
http://iganinja.jp/en/index.html
http://www.japan-guide.com/e/e4351.html

Toei Uzumasa Eigamura Movie Land, Kyoto
http://www.toei-eigamura.com/
http://www.japan-guide.com/e/e3934.html

Ise Azuchi Momoyama Bunka Mura (Edo Wonderland), Ise
http://www.ise-bunkamura.co.jp/language/english.html
http://www.japan-guide.com/e/e4305.html

Edomura, Nikko
http://www.edowonderland.net/
http://www.japan-guide.com/e/e3879.html

samurai and ninja experience
http://hisexperience.jp/index.php?option=com_content&task=view&Itemid=...

Anime and Manga:

Kobe Tetsujin Project
http://www.kobe-tetsujin.com/

Ghibli Museum
http://www.ghibli-museum.jp/en/

anime and manga shops:
Nakano Broadway:
http://bwy.jp/
Blister World Characters Store
http://www.blister.jp/
Mandarake stores:
http://www.mandarake.co.jp/en/shop

Others have offered some great suggestions.

Depending on the ages of the kids, you could combine the samurai interests and your own historical interests a little.

Yogen-in temple in Kyoto and Saisou-tei in Kurashiki are interesting places, because you can see the blood stains from real seppuku. It's historical, but also "cool" enough that the kids may find it fun. It's one of the fascinations many people have with samurai.

I'm not sure if it's still the case, but at Seki in Gifu Prefecture, they used to have a Samurai Sword smithing demonstration on the first Sunday of the month at the Seki Sword Museum. So I suppose it's possible that there will be a demonstration of Samurai sword making on December 6th.
Whatever the case, the museum is worth the visit.