Pony Fantasy VI Remake

1) Yes, those messages you will need to edit with a hex editor.

2) Sure, you'll need to check out the Runic Function in the C2 Dissasembly, specifically these lines:

C2/357E: A9 82 21 LDA #$2182
C2/3581: 8D A3 11 STA $11A3 (Set concern MP, not reflectable, Unblockable, Heal)

$11A3 is a set of flags for various effects, such as targeting MP, healing, and unblockable.
You need to clear the flag that targets MP. HP will be targeted instead. If HP isn't targeted, MP is, and vice versa.

In other words, you need to edit the byte that deals with those flags. (the A3 in that STA)
Looking at other examples in the Dissasembly, STA $11A2 seems like a good candidate to try instead.

3) Only 2 of the Tools use spell IDs that can be edited. Bio Blaster, and Flash. The other ones can be found within the items, but much of their attributes are coded in a way that FF3usME can't work with, and will require doing a bit of, you guessed it, assembly.
Previous thread regarding tools editing:
https://www.ff6hacking.com/forums/showth...ting+tools

(Be sure to search around on the site, I'm sure you'll find answers to some of the questions you have.)