Okay, I think I get it now - I'm supposed to be replacing the Steel Diver save not the ほぼ日の健康手帳 save. Good thing I realized that after I bought one of the other games and tried (and failed) with that >.< Off to try.
https://3ds.hacks.guide/installing-boot9strap-(seedminer)
Section II says JPN ほぼ日の健康手帳™ users should follow http://steelminer.jisagi.net/ instead of this section. Once those instructions have been completed, resume this guide at “Section III - DSiWare Injection”.
Instruction 1 in your link is...
I'm trying to follow the instructions at 3ds.hacks.guide on a JPN 2ds (11.8) using ほぼ日の健康手帳. So as instructed I'm following http://steelminer.jisagi.net/ but I get stuck at Section IV, because ほぼ日の健康手帳 isn't making a save file on the sd card for me to replace. It's saving on the console only...