Download BepInEx.
Unzip BepInEx into the folder containing "SecretFlasherManaka.exe".
A "BepInEx folder" will be created above the exe file that starts the game.
"SecretFlasherManaka v1.1\BepInEx"
BepInEx
Download the custom mission mod (SFM_custom_mission.dll).
This is the first reply in this thread.
Place "SFM_custom_mission.dll" in "SecretFlasherManaka v1.1\BepInEx\plugins".
Create a "CustomMissions" folder next to the BepInEx folder.
Not "BepInEx\CustomMissions".
It's "SecretFlasherManaka v1.1\CustomMissions".
Place all of the Warp_XXX.json files in the CustomMissions folder.