First, open Dolphin and go to Options->Graphics Settings
Then, under Texture Dumping select Enable, Dump Base Textures, and Dump Mip Maps.
Then, go to File->Open User Folder and navigate to Dump->Textures
Last, open the folder named after the Game ID of your game, such as SG4JDA for SCON4 or G4NJDA for vanilla GNT4.
Now you are in the folder where textures will be dumped to. As you open and play the game in Dolphin, new textures that are loaded will be saved to this folder.
To isolate a specific costume, we must start the game and get to a point right before the textures are loaded. So for example, if we want Choji costume 3 textures, hover over Choji. Then, delete all the existing textures in the texture folder like so:
Then, select the costume to load the textures. Dolphin will dump them out to the folder.
You can now modify these textures to make them custom and load them using the guide Dolphin Texture Loading.
Make sure to disable the Dump Textures Dolphin setting now that you are done, or else it will continue dumping textures while you play. This will slow down your game.