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Get JK Save Manager installed as a cia: https://github.com/J-D-K/JKSM/releases
Rename your .sav file to 0004000002C23200
Load up the game from the rom selector menu and go into JK Save Manager. Choose cartridge and export the save data.
You can delete the save file now.
Now inject the header and start up the game. Again rename the .sav file to 0004000002C23200
In JK Save Manager, go to cartridge and import the save
Now you can rename it back to what it was originally and enjoy