I never used RPG Maker, so I don't know what's (im)possible to do with it, but maybe you could make the lower floor and Nyarlathotep difficulty increase/decrease to a degree, depending on whether the player has the sword equipped and/or found the genie.
Now that I read your response, I know what your intention with the crafting components was, and it does make sense, but as a player without any insight into the development cycle of the game, I saw crafting components and expected that means there is crafting in the game. I don't know if RPG Maker supports the miscellaneous type of items whose only purpose is to be sold, but if it does, my suggestion is to make these flavor items that type. Then, introduce the crafting components in the same episode you introduce crafting itself in. If that's not possible, maybe add a notification to this first episode that crafting will become a thing in the future.
The biggest problem with the first desert area was that I was running around in circles, and was interacting with the same cacti a lot of times. Adding a few distinguishable features to the first desert map would be great, so people know they'd already visited an area. Lacking specific directions is fine since El Cid was there by accident.