TheTechMatterAnswer: Japan Travel & Internet survival guide

Choosing the most appropriate period depends on your commitments (obviously), on personal preference (if you like more heat, cold, or something in between) and on the cities you have to visit in Japan.
So the main factors to consider are the weather and things to see in different cities.

In fact, for example for the island of Hokkaido the weather is usually subarctic and island of Okinawa has a subtropical climate while in many parts of the main island (Honshu), where are located the most famous and populated cities there’s mediterranean climate.
On this site of Meteorological Agency of Japan you can find an indication of rainfall and the  weather state of this year: http://www.jma.go.jp/jma/en/Tourists/indexe_tourists.html
In this other website there are some tips and guidance on choosing the most appropriate period according to your personal tastes: http://www.japan-guide.com/e/e2273.html

After analyzing those sites and others, seeking information to satisfy my personal tastes I have come to the following conclusions:

• If you like a climate hot, very hot, muggy and humid (I like it), choose a period from mid-July to end of August.
• If you want to see the cherry blossoms choose the month of April.
• The cherry trees will not flower all at the same time, then you risk not seeing them even if you go in April.
• The period from June to mid July is a month for which it’s raining in most parts of Japan. Usually this small “rainy season” (tsuyu) ends in mid-July but clearly this depends on luck.
• The month of September is the month of typhoons, that usually have a strong impact on the southern islands (Okinawa Kyushu, Shikoku), but I’m not so sure, so I absolutely excluded it.

After deciding the possible months for your holiday dates, select days more precisely according to the festival (matsuri) and  opening dates of the attractions you want to see.
To choose the attractions I remember you websites of some cities:

http://www.osaka-info.jp/en/search/detail/event_5889.html

http://www.tourism.metro.tokyo.jp/english/

http://kaiwai.city.kyoto.jp/raku/modules/english/index.php

http://www.welcome.city.yokohama.jp/eng/tourism/walking/1200.html

http://www.kanazawa-tourism.com/

Many events can also be found in the JNTO website: http://www.jnto.go.jp/eng/location/festivals/index.html
However be careful because for example Kumata Summer Festival in Osaka, although very beautiful and characteristic is not indicated in the JNTO list.
So I suggest you refer to the site of the city that you have to visit and ask for confirmation, directly to that site,  by e-mail the start and end date of an event .