Monsters Countering One Attack As If It Were A Different Attack

Right, I just tested it. Make sure you target the character (FC 17 45 00. Do NOT use F1 here. It doesn't work for some reason.) that initiated the attack. The game seems to be loading the most recently stored target for certain counters.

Okay, so if I'm understanding your post correctly, and forgive me if I'm not - even after working on this hack for a full year, albeit slowly, I still feel fairly new to this, so I was a little confused at first and simply guessed based on the part that I could understand of it (the only "F1" in the counterattack portion of the script that I see, the "Targeting: use normal targeting" part of my Blitz counter, I tried removing entirely, and it had no effect on the bug, as it still triggered the same way as before, so I tried interpreting it another way) - I need to put the "FC 17 45 00" line immediately after the "FC 05 00 00" line, right? That did indeed make Ultros respond to NoiseBlaster with an Ink directed at Edgar. Though it also made Ultros respond to Potion in the same manner. (He also responded the same way when Terra cast Cure on him - spat an Ink in her face.) Surely the game is not *supposed* to trigger counterattacks on healing spells/items/etc., is it? (Spells and/or commands designed specifically to heal don't sound like they should be classified as "attacking" the target. Or does the game see any sort of targeting whatsoever as "attacking" the target? Elemental absorption would be another story, of course, as Ice3 is still an attempt to attack the target, regardless of their ability to nullify or absorb the attack.) Or did I misunderstand your instructions?

That does sound like the FC 05 bug in action.

I better find a way to double check if I applied the patch, then - because I'm...99% certain I applied Master Zed's patch. Which makes me concerned the base ROM I used for my hack is somehow not compatible with the patch. (Headered if the patch is for a headerless ROM, 1.0 if it's for a 1.1 ROM, or whatever else it could be).
EDIT: I think I might have indeed applied the patch. But to make sure of things, I went back a couple of versions, just far enough to *know* I hadn't applied it to yet, applied the patch, then went to test Ultros again (after updating his AI again with FC 17 45 00 line) - now he's...I'm confused.
Quoting Master Zed's guide: "Another FC 05 bug (see above for the first and most evident of these two bugs [referring to the "FC 05 becomes an omni-counter after its first strike" bug]), FC 05 only retargets who to counterattack if damage is done." That's not quite happening here. Ultros is responding to NoiseBlaster by hitting Edgar with Ink. (As well as Cure by hitting Terra.) The target is set correctly, and it isn't using the Pearl, Fire, or Blitz counter, but it's still not supposed to be countering in the first place. Did I do something wrong? It looks like Master Zed's patch is correcting half of the behavior, here - but only half, and the unimportant half at that.
If I use AuraCannon then Cure, Cure is countered with Ink. Same with if I use Pummel instead of AuraCannon. If I use AutoCrossBow, BioBlaster, or Attack instead, Cure is ignored. If I use Fire then Potion then NoiseBlaster, Potion is countered with Ink, but NoiseBlaster is ignored. If I use Fire then NoiseBlaster then Potion, NoiseBlaster gets countered with Ink, but Potion is ignored. [EDIT2: Also went back and tried this with AuraCannon, seems to do the same thing, only countering a single move that it shouldn't then properly ignoring the next one. Same with Pummel.] It's no longer omnicountering...after it omnicounters once, anyway. That does NOT sound the least bit right. Have I unknowingly broken something, over the course of making this hack?

It is entirely possible you've overwritten something in C2 in the FC commands. I'm at a loss at this point.