utilities will run you 15,000 to 20,000 yen/month depending on the season, your location, your type of apartment, and your lifestyle. (guest houses won't charge for this, but you may have to provide a 25,000 security deposit)
food will run you 30,000-60,000 yen/month depending on your lifestyle and appetite
phone will run you 3500-8000 yen/month depending on landline vs. cell phone, and on how many calls you make (even local calls cost money here).
local transportation could run 20,000 to 25,000 yen/month.
Want to stay longer than 90 days? Get a proper visa. Student visa, cultural visa, work visa. Requirements vary.