Help with menu...

As long as you keep the Tools icon there before the name, they shouldn't disappear. All items in the item list except the regular items like Tonic/Antidote have icons that the game uses to sort them in the menu. If you remove the icon, they will disappear when you hit arrange because the game has no idea what do do with them anymore.

Regular Items by default do not have an icon, well, they instead use $FF which is a blank space, but not a spacebar space, as that is $00 I think - the game get's confused and cannot read it and the item will vanish upon arrange.

The normal Tool icon in hex is $E5, so if they are really broke you can go into the hex and locate the tool names, and put $E5 before the name again...or just do it with USME lol, I see no reason why that wouldn't work.