Rules mention the requirement of playing the freeware Japanese version of the game. I can do that through the nintendo DSI (Different from the DSIware port from NICALIS) if i submit a run via DSI would it be accepted?

In general, we don't accept runs of unofficial ports/releases of the game. If you want to play on your DSi, feel free to run the DSi version by Nicalis and submit that to the Cave Story+ leaderboard (https://www.speedrun.com/cave_story_plus).

Bet