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The Poccil kit has originally made for Gen III mechanics, so you can't run in buildings like since Gen IV.
To put this in your game, in Walk_Run delete the below yellow highlighted code.
If you also delete the blue ones, you can run while surfing and diving. It's the same thing as running on ground, but the graphics won't change for the running ones.
def pbCanRun? return Input.press?(Input::A) && $PokemonGlobal && $PokemonGlobal.runningShoes && ( pbGetMetadata($game_map.map_id,MetadataOutdoor) || ($PokemonEncounters && $PokemonEncounters.isCave?) ) && !@move_route_forcing && !$PokemonGlobal.diving && !$PokemonGlobal.surfing && !$PokemonGlobal.bicycle end