I finally got to playing the game and I think I found the bug in the version 4.0. The same one as above.
After getting Hinokagutsuchi and entering the Equip screen it looks like that:

But the main problem, after that bug occurs, the game starts behaving erratically. On the field, characters can move only up or down, and the terrain descriptions changes to types not present on the map:

Thankfully, once Hinokagutsuchi is equpped, the Equip screen gets back to normal. And the rest of the game fixes itself after using internal save, resetting the game and restoring the save.
The bug encountered then using the SNES9x 1.60. The ROM is correct one, I checked the hashes using the NSRT. I use IPS version of the patch, with the emulator soft-patching. And if that helps, an srm file with Hinokagutsuchi and that bug.
https://drive.google.com/open?id=1PLILjD0yy88ryqi_e6DuoFPirslV1vRR
November 11, 2019, 05:53:25 am - (Auto Merged - Double Posts are not allowed before 7 days.)
Finished the game today. Thanks again for the translation.
I'll also use this opportunity to report another small bug. A slightly broken line in the final sequence of the best ending. It is a
spoiler, so I'll post the screenshot as a link.
https://postimg.cc/FdZz8SF7