In Tokyo and Kyoto I stayed over at K's House (Backpackers Hostel), cheap rate^^
http://kshouse.jp/tokyo-e/index.html It has many branches in other towns too. Very clean and comfortable. It has many facilities as well.
From town to town, we go by night bus. We avoid riding Shinkansen to save cost.
From Tokyo to Kyoto, we reserved this bus:
http://www.123bus.jp/You can buy tickets even from 2-3 months before, and if you make reservation online, you have to pay directly with credit card account. 4700 yen per person. Not really a comfy bus for a 9 hours trip, but it was okay.
*WARNING* On the bus terminal, do not look for 123Bus, the bus coming have a different name. We almost didn't get to ride the bus, since I kept thinking the name is suppose to be 123Bus, lol XD Good thing my friend decided to ask the bus driver.
The bus terminal is in Sunshine Bunka Kaikan at Ikebukuro, you have to ask people around to the find the place. It was quite hard to find.
From Kyoto to Nagano, we reserved this bus:
http://bus.hankyu.co.jp/highway.shtmlTickets can only be reserved 1 month before. The payment HAVE TO BE DONE at convinience store in Japan, and the limit time was only 5 days after online reservation, so I had to ask my friend's help, who was living in Japan, to do the payment first. 5200 yen per person. Much better than the previous bus, spacious, we get slipper and blanket. A very comfortable 6 hours trip^^
*WARNING* The bus terminal was right in front of Shin Hankyu Hotel, near the Kyoto Tower. Sometimes, it has a different bus name too.
From Nagano to Tokyo, we ride this bus:
https://www.highwaybus.com/rs-web01-prd-rel/gp/indexTickets can only be reserved 1 month before. The payment must be done at convinience store in Japan, but the limit time is the departure time, so we can do payment right before departure. 3400 yen per person. It's Matsumoto - Shinjuku line. It took 3 hours to reach Tokyo. And oh, this is not a night bus, it was in the afternoon, and there's a bus from Matsumoto to Shinjuku in every hour.
*WARNING* Matsumoto Bus Terminal has many platforms, you have to enter the terminal first (there's a supermarket inside), and find guidance on what platform your bus is, and where the platform is.
It might be a bit difficult if you can't read Japanese at all, if that's the case, then you just have to ask around as much as possible.
In Nagano, I stayed at ALPINO, Love Generation's filming location:
http://www.alpinonet.jp/ Rate 8000-8500 yen per night per person, incl. breakfast, dinner and onsen.
The owner was so kind that she gave me a discount for no reason^^
Actually, you might want to try PEEPOLO too:
http://peepolo.com/It was the filming location of Riko's family's house. But I picked ALPINO, because it was cheaper.
To get to ALPINO, we have to reach Matsumoto city (Nagano prefecture) first. Either JR Matsumoto station (by shinkansen) or Matsumoto Bus Terminal (by bus). Depend on the ALPICO bus (Matsumoto Railway co.) schedule, you can ride a bus directly to ALPINO OR you have to ride a train first to Shinshimashima station, and then ride Alpico bus from there, and get off at Kanko Center Mae bus stop.
Check ALPICO bus schedule here:
http://www.alpico.co.jp/access/route_k/norikura/index.html Oh yes, as for TOEI Kyoto Studio Park, you can check out the site here:
http://www.toei-eigamura.com/ Entrance fee is 2000 yen. But for me, it's totally worth it!^o^
What else?? I think that's all. If you have any question, don't hesitate to ask ne ^_^