Edit: Nevermind. Finally got the program working. Now I'm just trying to figure out what exactly I'm supposed to do with it.
If I'm not too late, allow me to explain: If you only want those 3 equipment, then edit whichever equipment you want (I recommend the regular Protection, Speed, and Brawn badges). Since the stats can't simply be zero, you must edit each badge so as when you equip all 3, they will equal zero. Then be sure to save the changes.
Just realized, you might have meant you don't know how to load the save lol. You must use savedatafiler to extract the save and load the system_data.bin from the save. If you have a .3ds/.3dz version of the rom, you must follow liomajor's .3ds/.3dz to eShop Save guide.