You unfortunately can't mod saves for any game past the 2.1 firmware release (any game after MK7 and SM3DLand)
3DS games are encrypted with an XOR key as you know, but newer games use a different type. With old games, the key repeated every 0x00000200 or so but with new ones, each section is inconsistent, ranging anywere from 0x00000100 to
0x00001000 so it is at the moment impossible to decrypt except by hand.
And then you would have to know how what to modify, how to create a new checksum, and then encrypt everything by hand again. And it all has to be done by hand. So until we have a 3ds firmware emulator or something that can use 3ds encryption patterns, there is no way to modify 3ds games released after the 2 games listed above.
Though I hear the 3dsfuse tool is close to reencryption of newer saves.