there are only two completely unused special sizes in the entire game
Which two, specifically?
B1 and B2. They're just little 1x3 rectangles in the air by default (and no, they're not Baigan's arms).
... or you might want to whip up a new version of FF4kster that allows a hacker to edit the special size table
Done and uploaded. 
Oh, wow. Cool!
Taking a quick break... Did you check to see if Kainazzo's transition uses one of those weird numbers with one or two of the upper two bits?
How do I check this? Which byte should I be looking at? In FF4kster, Cagnazzo's script just says "change sprite to 19" which is exactly what I put into Alichino's script...
No, that's what I meant, so that's not the problem...
That's all I can think of now. If not, if you wanna send me a ROM (or patch) I'll take a look at it.
Hm, I'd like the details of the game to be mostly a surprise and I'm pretty far in plotwise so I'd prefer to talk it out if possible... though if it comes down to it I don't mind sending you a copy. In the meantime I'm attaching a "before" and "after" screenshot....
If you have some kind of sandbox rom handy, try this and let me know the results:
- Replace the graphic pointer and size byte of a boss monster (on mine I replaced Q. Eblan) with Cagnazzo's template (he should be in the list of templates)
- Change this monster's AI to contain an instruction telling him to change sprite to 19
- Replace one of the underground Formations and put the new monster in there (I used Formation 502)
- Set up a way to fight him in the underground and have at 'er
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That's cool, I can empathize 100% on that point. But please understand that that means it will take me longer to get to trying to figure this out. I do have some work on my own project I intend to do this weekend.
However, this gives me pause...
And yes, the "change sprite" process does cause him to change back to Cagnazzo's palette... it also seems to make porom throw her arms up and selecting Edge's magic menu to hang the game.
This sounds precisely symptomatic of a bugged battle script.
If you put two uncooperative actions together in a monster's AI without properly separating them (like, with "Wait"), then when the monster gets to that part of its script, the character in the middle will freeze in their "dodge" stance and the game will hang when you choose your next action.
Also, are you remembering to make that second sprite transition back to
Alichino's initial spriting instead of Kainazzo's? That might explain why he's reverting back to the wrong palette...
Anyway, I promise I will look deeper into this this weekend. I won't leave you hanging, but I need at least a few hours to devote to my own stuff before I start playing around with a blank ROM to try to match what you've done, k?