Create a font for use with the Japanese keyboard
The conversion of letters into glyphs is done by the keyboard, not by the font.  So there is no need to create a font, unless you want to generate glyphs not in Unicode.  If you want to type two letters and have it turned into an already existing glyph, there are lots of ways, including:


use the US keyboard and make entries in the replacement grid of system prefs/keyboard/text.
create a custom keyboard layout with the Ukelele or Karabiner apps.
create a custom input method as mentioned in OS X: Create and use your own input source


If you want to duplicate the mechanism of the Japanese keyboard, you will need to examine the workings of system/library/input methods/JapaneseIM.app

If you want to create a font with custom glyphs, there are various apps for that like Fontlab, Fontforge, Robofont, Type, and Glyphs.  Whether or not you can make the Japanese IM use a custom font to generate your custom glyphs you would have to test -- I have not seen this done by anyone before.