I will share my trip experience during Nov'16, Is a 8 day trip. I used around rm4000 per person exclude accomodation and flight.

You might want to consider travel to kyoto first then osaka, so you no need repack your luggage.

I stayed at airbnb for the whole trip for kyoto and osaka, I able to find around my budget around RM150-220 per night, you might need to read carefully on the description, as some of the room doesn't include bathroom, you also can save some money if you get wifi egg from the host.

Most of the station will be like 1-2min to each station but will be cramp during morning working hour.