Let's try to rule certain possibilities out:
- Try starting the game without any shop.bin at all. Your Shop menus should be a huge mess now, but don't worry, this is reversible by putting the shop.bin back in (always have a default shop.bin ready just in case). If everything is still normal without shop.bin, there is definitely something wrong. If you can see the mess too, it's all good. Move modified shop.bin back to menu.fs twice in a row (preferably per drag and drop, as it saves some clicks) and start the game.
- Do you accidentally load a save with Tonberry's Familiar Ability unlocked? If so, delete it by using Amnesia Greens and check the Balamb Shop contents again. According to your changes from above, it should only offer G-Potion, with the rest being invisible until you have Familiar.
- Don't forget to save your changes made with Translhextion before moving files back to where they belong.