[BizenKiyomitsu]

Hello Som-san, welcome to Japan beforehand.

I suggest you to take Shinkansen Train. It will be almost 2 hours from Kyoto to Tokyo. (If you take Nozomi or Hikari.) Also it might be good experience for foreigners. Both in Kyoto and Tokyo we have many cheap and safe plcases to stay.

As for JR Rail pass, as long as I take a look at your Trip plan, you do not have to buy it.

Odaiba, hum, how about "http://www.caretta.jp/english/" ?

As for Mar. 30th, you'd better go to Arashiyama and Eigamura than Kitano Tenmanngu and Nishiki market.

Just FYI, you will come to Japan in the season of SAKURA. So, April 3rd and 4th would be ridiculously congested everywhere.

Above is my comment. Enjoy your stay (^ ^)v