I worked on such a dictionary for my master thesis. A researcher I'm working with gone as far a building a whole crowd sourcing platform to correct OCR output from a Japanese-French dictionary, compiled by Cesselin. You're more than welcome if you can contribute to this language pair. http://jibiki.fr/
See my other comment above about Pingtype - some friends have asked me to make one for Japanese-Chinese, or Japanese-English, so I'm making a note of possible data sources (Naruto, One Piece, One OK Rock, Ellegarden, Hillsong Global Project, 新改訳聖書). I've made a note of your dictionary project, so I can look into it in future!
I sympathise with his emotions: "What a beastly labour of hand & back bending, besides mental toil & anxiety"
I'm currently working on a machine translator for Chinese dialects, including traditional & simplified characters, pinyin, bopomofo, literal English translation using a dictionary, and parallel English text. I'm adding Taiwanese and Cantonese dialects now, with their own romanisations. I'll publish it here on Hacker News when my friend finally translates the documentation.
Most notable one is conflation of vowel [イ] and [エ]. Often both are denoted with "i", sometimes one of them is "yi". In modern American English the sound /i/ falls in middle of Japanese イ and エ. I'm not sure in this case that it's because of that, or Ryukyu dialect had shifted vowels.
セ is denoted as "she" (usually "se"). This variation of consonant appears in some Japanese dialect.
ヒ is denoted as "fi". Might stem from old Japanese pronunciation.
Curiously, ヰ is denoted as "i" and ヱ is denoted as "yi/ye/e". Usually they are "wi" and "we", but those pronunciations have been lost in modern Japanese.