Nice project; I hope it goes through! I believe you forgot two more occurrences, though. In Paper Mario, when you jump in a pot in Bow's Mansion, you turn into an 8-bit Mario. While you're an 8-bit Mario, the theme plays. The same thing occurs in Paper Mario The Thousand Year Door, except you fall through a hole in a ventilation duct in the X-Naut Base which leads to a dressing room. After opening the curtain, Mario and his partners turn 8-bit. While they are 8-bit, the theme plays.
I'll check back often to help out, and I would really like to see when this project gets completed!