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Mr. Fuji is at the very back, standing alone.
yes, after you beat red go to the fighting dojo and the karate king will be standing there with mr. fuji, you have a double battle and if you win mr. fuji leads you down a secret path in the fighting dojo and that leads to the house of memories lower rooms. there you will also meet team galactic leader Cyrus.
In the grave house on the bottem right.
Use the itemfinder at the spot where mr fuji once stood at the top of Pokemon tower you should dig up a soothe bell. where mr fuji was standing use your itemfinder there
Get the pokeflute from Mr. Fuji in Pokemon tower.