You'll be done with the hack after reaching a certain room and then back-tracking to the ship, the room in question may not be immediately obvious but aim for 100% item collection and you're sure to pass it!
This is the fruit of the last two day's labours. It uses the charged space-time beam to jump to the super missile count in RAM, and uses that to jump to OAM. The OAM in this game is very fickle, but I managed to get it to jump into the middle of the gamepad auto-read registers, where I built up a total control loop, letting me execute arbitrary code at a rate of 4 bytes per 6 frames. As a test-case I set the game mode to 26 and returned control to the game, resulting in the ending sequence.
This movie is based on the 100% TAS. I had to truncate the part where I walk to the green pirate room in crateria in order to start a new movie with the correct number of controllers. The resulting movie is therefore very short, and the interesting stuff happens in a fraction of a second. It is best watched frame by frame - ideally while tracing in a debugging emulator.
This was done in snes9x 1.43-rr. It should be ported to a more capable emulator.