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Asia81's guide on decrypting and re-encrypting games is what you want to follow. After everything is extracted, you use PK3DS to make your edits. You can try Ohana Rebirth for texture edits but that's not something I'm knowledgeable about. Once you've made your edits, you simply continue to follow the guide.
https://gbatemp.net/threads/tutorial-how-to-decrypt-extract-rebuild-3ds-cia-cxi-files.383055/
https://gbatemp.net/threads/tutorial-how-to-decrypt-extract-rebuild-3ds-cia-cxi-files.383055/
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