Okay, first off, thank you Canade for the translation. 
Next, something i've been looking at as well:
After a little trial and error, i can confirm that what you're looking for is two files. You'll have to copy them back over from the original if you want to disable the cheats.
/data/Classes.json <-- The stat boosts for your character. Replace with original to have 10 in everything again.
/data/Map022.json <-- This one was a bit harder to guess, but i reasoned that this had to be something the map gave to you, since i had only copied in the maps when the items popped up. A bunch of copy pasting later i found the map used in the intro, and 'lo and behold, replacing it with its original prevented the game from handing over the modded free items.
Keep in mind however that this does NOT fix your starting gear, since that was replaced inside multiple other files (likely Weapons, Armor etc.) which would be a bit harder to find. There is a workaround however in using the original /data folder (because you DID back it up, right?), starting a new game (as long as you've got the /js files from the mod, the translation should still be mostly fine) and making a save. Then exit the game, copy over the /data folder (except Classes.json unless you want the stat boosts, Map022 won't matter anymore since that trigger has passed) and you should have a patched game with non-cheated gear and stats.
I think that... pretty much narrowed it down?