Depending on which scenario you start with,(which doesn't matter) you need to play through to the second scenario and finish it with a grade ranking of A. If only that solved the problem...Anyway save the file, and start over beginning with the scenario you started out with first. Play through the games two more times, each time ending the second scenario in the grade rank of A or higher. After you save the third game of the second scenario, you should unlock Tofu. Piece of cake...

At least, that was how you did it back on the playstation version. There shouldn't be anything involved with the Ex Battle because that is not apart of the ORIGINAL game mode. Don't save it on different slots...its supposed to be one continual save file. You should have already unlocked the Ex Battle with the first second scenario grade A ranking, not to mention various unlimited weapons. If this doesn't work, beat the second scenarios with an S ranking.