E-1: How can I automatically set the coding system to JIS when I

 move to mail-mode?

If you are using RMAIL or VM, mail-mode-hook can be utilised. Add the following lines in your .emacs file.

  (setq mail-mode-hook
        '(lambda ()
           (cond ((boundp 'NEMACS)
                  (setq kanji-fileio-code 2))
                 ((boundp 'MULE)
                  (set-file-coding-system *junet*)))))

If you are using MH-E, mh-letter-mode-hook can be utilised. Add the following lines in your .emacs file.

  (setq mh-letter-mode-hook
        '(lambda ()
           (cond ((boundp 'NEMACS)
                  (setq kanji-fileio-code 2))
                 ((boundp 'MULE)
                  (set-file-coding-system *junet*)))))

Usually you do not have to do these settings by yourself, as mule-init.el already contains necessary configurations.