Been there once and hostel usually around 2,200-3,000 yen in Tokyo, Kyoto around 2,000 yen. I know this really good one in Kyoto, just reply in this message if you want to know who is my contact in Kyoto. Airbnb you can check the site lah, but shouldn't be far off from the price range I mentioned. Then for food, usually a budget meal is 600 yen, but you can get something for 950 yen and that is like double the portion, very filling and food quality also good. Transport, you can get subway passes in Tokyo that cost about 1,500 yen good for three days, can ride Tokyo Metro and Toie lines unlimited, then in Kyoto there is  Bus Day pass for 500 yen, unlimited rides also.

So, let's say you stay in either Kyoto or Tokyo for three full days, you are looking around 13,000 yen basic. I always allot 20% more of my minimum expenses because I eat a lot and I get distracted by all those small shops that sell cute things, so I suggest you budget around 16,000 yen or 583 RM. Cheap, right?

Yeah, Nara is beautiful. Yes, I blog also. You can check my itinerary here-> http://wanderlust.tripovo.com/stories/how-...-12-days-all-in

And to answer your question about the flight, usually off peak season is summer, but that is also the time many Japanese go for holidays, so it is a bad time to travel. Hope this answers your question!