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Hint: Squirtle is on the B2F (middle floor; NOT on B3F!) of the Seafoam Islands (running, not surfing or fishing). Kabuto is in the entrance floor of the Icefall Cave (Surfing). Pinsir is at the Three Isle Port.
Here is an updated locations list. The items list may not be updated, but the Dusk Stone location was fixed.
Notes: * means this Pokémon has a 1% encounter rate, and ** means this Pokémon has a 2% encounter rate. Also, you can get stones at Battle Frontier after beating the game.
I have no idea...