Here's the body of my email to him asking the questions (we had talked some before, but the content of those messages isn't important):
Okay then. If you could please answer these questions, then...
1. Did you write the music for Cave Story for any particular instrument, or was it written for the organya format directly?
2. What (musical) pieces were easiest and hardest to compose?
3. What is your favorite piece?
4. Are there any pieces you would have changed if you had access to a more complex format?
5. Was there any overarching theme to the soundtrack, or did you write each piece separately from the others?
6. Why was the Plantation music chosen as the title screen music?
And some more questions unrelated to the research paper, that I would still like to ask...
1. As you may or may not know, Balrog's catchphrase was translated "Huzzah!" by the fans and "Oh Yeaaaaah!" by Nicalis. Which do you consider closer to your original vision (assuming that the difference is noticable to you)?
2. Did you expect Cave Story to become as popular as it did?
3. Is the Cave Story sequel you've hinted at actually a prequel?
4. Do you know the full backstory of Cave Story, or were you just inserting vague references as you went along?
I'm waiting for a reply.