The Verdict: Not eligible
Naturalisation for distinguished service needs a vote of the Diet and is effectively never used, so it is not a route to plan on. Look at the highly skilled points system through our Skilled Migration route for Japan.
The Nationality Act lets the Minister permit naturalisation for special distinguished service without the usual conditions, but only with the approval of the national parliament. There is no form or office to apply to.
The highly skilled points system scores academic background, experience, income and age, with bonuses for Japanese ability, a Japanese degree, research, patents, national qualifications and priority fields. At 70 points you get a five-year stay, spouse work rights and permanent residence after three years; at 80, after one. Research and priority-field bonuses are often where a real contribution to Japan scores.