The next step involves the Citric Composer. Install it, run it, and select the Isabelle tool. You can use this tool to import your new .wav files, export to NX Wave (.bfwav), then use Tools→Game File to Game File to re-process the .bfwav, making sure the version of this new file is the same as the .bfwav found in the base game's files. Make sure the new files has the same name as the files you wish to replace, and store them in a separate folder.
Next we use BotWTool's Bars Injector. This is a python script, meaning you need to have python installed. The readme describes how to use it, using the previously described original .bars, the extracted bfwav folder and the folder with your new bfwav files. The script will skip any files that do not have new versions. If all is successful, and new file called output.bars should be created. Place it into the SD card's [GAME_ID]/Sound/Resource folder, rename it to the file it is replacing, and play the game in an attempt to find a place where it plays. If something has gone wrong, the game will crash upon trying to play the new SFX. Otherwise, enjoy your new SFX.