1) Completely depends on where you go. You will pay the dormitory fees. The fees are generally cheap.
2) 172,000 yen is a ridiculously good living allowance for a student. Congratulations, you have probably the best scholarship in Japan.
3) You get a free plane ticket sent to you. You will receive 25,000 yen once you arrive. This will be more than enough to get you to Ehime. Your airport will likely be Kansai International, though it may be Narita for some reason (I seem to remember everyone coming in by Narita when I got the scholarship). In either case, 250,000 will be enough or close to it.
Don't bother booking transportation in advance. Either someone from the university will be there when you arrive, or go to the ticket counter and explain where you want to go - train tickets are exceedingly easy to buy.
Bring at least 150,000 with you when you come - it is important insurance until you get your first stipend.