Rail Pass for a student exchange

Hello,

This summer I am going to do a student exchange in Akita for about 6 weeks, and I am wondering what is the best deal for purchasing this rail pass.

1) I am thinking of purchasing two 21-days pass or (one 21-days and one either 7 or 14-days). I will most likely travel during the weekends or weekdays after class. Is that a good deal?

2) When I purchase the tickets, where can I activate them? Is it available in both Narita Airport and Akita city (when I want to activate my second pass)?

3) In case I realize that the pass(es) expire before the end of the exchange session, is there any way I can purchase another pass when in Japan?

4) Just want to make sure: the pass is only valid for JR railways, ferry, and buses only. Therefore, if I were to use local, non-JR public transports I still need to pay their respective fee. Is this correct?

Below is the general itinerary:
June 16: Arrive at Tokyo, spending a night
June 17: Departure to Akita
June 17-Late July: Exchange session, possible travelling in between
Late July: Return to Tokyo, Return to home country

Thank you. I am looking forward to your reply.

-Alvin