I love it when friends come to visit! My apartment has two rooms, and I have a comfortable two-person sofa bed for guests. Hopefully, the links below will help you organise a nice stay in Japan :). Of course, before you book a flight, please check if I'm actually around at that time ;).
When to visit Japan: any time except during summer. Especially July and August are just not very nice at all, too hot and humid! Although north Japan may be better. Autumn and spring are the nicest seasons to visit, but winter isn't bad either.
Google Flights will be helpful in finding the cheapest/most convenient flight to Japan. My home is close to Kansai International Airport (KIX). Generally, a ticket from Amsterdam to Osaka may cost about €600 with a short layover (mostly Frankfurt or Helsinki), or a little more with a direct KLM flight (lowest I've seen is €650, during "Werelddeal Weken").
Japan rail pass allows you to order a pass for all JR trains, including the Shinkansen high-speed trains, valid for 7, 14 or 21 days. You can also buy cheaper region-specific tickets for regular JR trains. If you intend to travel at all, highly recommended (especially Shinkansen trains are very expensive if you buy them here)!
Kansai tourist information center (located at Kansai Airport) has a lot of tourist information about the Kansai region (which includes Kyoto, Osaka and Kobe), as well as reduction coupons. Worth getting!
More pages will be added when I come across them :).