Go to the link I provided you and extract the archive at the root of your SD card, then put it back in your 3DS and launch the homebrew menu using tubehax/ironhax.
Search the "Savedata Manager" homebrew in the list (it looks like LinkMain's picture), launch it then use left/right arrows to select pokemon shuffle and press A.
Glitch screen, then press A to copy shuffle's save on your SD card.
On your computer, extract Pokemon Shuffle Editor.exe and launch it. Transfer your savefile from SD to your computer (it's "savedata.bin" in the savedata folder), copy it at 2 different places to have a backup in case things go wrong. Remember not to launch shuffle from the moment you extracted your save.
Open your save using the editor and edit it as you wish, then save it and copy it back to your SD card (overwrite the original file). Make sure you don't copy back your unedited backup file.
Power on your console, launch homebrew menu then SDM, select shuffle and this time press B after the glitchy screen to import your edited savefile. Once done, press X to quit SDM, then Start then A to get back to home menu. Launch Shuffle, your edits should now appear in game.