Pony Fantasy VI Remake

1) To enable Umaro access to the Gauntlet/Genji Glove auto equip feature like the other characters, that is happening here in C3:
C3/9EF4: C90D     CMP #$0D       (Is it Umaro?)
C3/9EF6: F007     BEQ $9EFF      (branch if so)

EA EA EA EA should do the trick. I can't think of any adverse effects from doing this. You can increase it to 0E if you want instead.

2) As for the Resilient Morph issue, that is how version 1.0 of it was. So that's what must be in the gogo magic code as well. You should look into updating to the latest version:
http://www.romhacking.net/hacks/1138/

However, I think without reverting the old resilient morph data the damage change will still happen, so you might want to contact HatZen here via PM about what to change back since version 1.0 of the patch is not available to check and I forget exactly what it was as it's been a couple years. As for the latest version being compatible with the gogo magic code, I'm not sure, but I think it is okay I am using the latest version of Resilient Morph with it and don't remember needing to update anything with gogo magic, but my memory is pretty bad at times...

Or was it that you used Resilient Morph patch already outside of the gogo magic code, in order to make the gogo magic patch work? But no, then that would be the latest version... Hm I can't remember what it was now but I'm wondering if you wanted to use Resilient Morph or got stuck using it as a result of the gogo magic patch? I thought everything Resilient Morph could be removed/left out of the gogo patch and everything else would still work, I don't see why not. Unless you like it, and just want to change the double damage received part, then yeah HatZen could help you revert that.

3) For your event there, it's hard for me to tell without having it here to look at and test, but it definitely sounds like you're still activating the game over subroutine somewhere after that battle, or else it would not happen. The subroutine after pretty much every battle:
B2    Call subroutine $CA5EA9
must be being called in there somewhere after that battle...

Did you include that whole code you posted from the moogle battle? Most of that wouldn't be needed and would definitely mess things up, but I'm guessing you meant you used just the 'take HP and add 1' and remove status parts and not the whole thing you pasted here?

Also I'm a bit confused about that subroutine to CA/658A at the end. That's just a jump to an FE and that's it? This wouldn't make much sense if there's an FE right after this to end it and I can't think of a reason for doing this, so I'm wondering if there's more code there or if you meant something else. It also look like important tile replacement code at that address, unless you removed/moved that. I'm just confused overall about this subroutine.

But yeah if you're getting a gameover, the gameover subroutine is still being called somewhere there, through one of the subroutines you are calling that might branch to it, or some code that is left in - look for that death subroutine. Also it probably goes without saying but be sure and test from before the battle, not from a save state during the battle where the gameover routine might still be being read if it was before you edited it out.