(SPOILER ALERT? The information below gives away info on the hack from Mysidia to KluYa's Shrine)
Milon... what else can I say...? Milon... well let's start from where I left off. I love that Porom was given Stone, it gives her some real offensive and crowd control power (even able to wipe out all enemies at once) and the Clones of the Twins was an Awesome feature! I loved that! Defeating them also yielded some great stuff for the mages, a full new set of equipment could be grinded from them. At first the player is nary prepared for the fight, and if they choose to fight the twins with a fresh Palom and Porom they are bound to lose, it's nice that you didn't have it give a gameover, very pleasant touch. I trained them up to roughly 18 then headed up Mt. Ordeals, this is where the Dark Armor weak to Dark really becomes apparent, from normal enemies to the bosses, everything is out to get Cecil and his weakness to them. This is also a Very smart move on your part, to an unprepared player this place is a Deathknell. The place relies 100% on the Twin's abilities to equip Bows and White Arrows.
Every enemy, aside from Lilith are weak to Holy, but nigh immune to magic, making the newly acquired Tellah next to useless (give him a Cure Staff and let him heal) The smart thing to do would have had both twins on Crossbows, but... I didn't use that. Instead I went up the mountain with only Porom on the bow. Not knowing how things were going to go. Well I reached the top mostly by running, but Palom and Porom had both reached Level 20, giving Palom Virus (or maybe it was 21?) without Virus I think that Milon would be even more difficult.
So onto Milon... as mentioned earlier, I grinded the Evil Twins for their Wizard set and Rune Rings to give to Palom/Porom/Tellah, this seemed to help out immensely, now the first form of Milon did give me a lot of trouble as this was my first encounter with the Magic Immune Ghasts, (imagine my surprise when I saw something that Slow Didn't work on) eventually focusing my resources on Palom I managed to defeat Milon, and the Ghasts didn't die with him. I had thought they were invincible, since I had only the Dark Sword and magic, until I recalled that I had the Crossbow and White Arrows, and placing a PowerDrink on Palom he was doing well enough damage to kill one in three turns, so a bit of that and the Milon formation was dead..
Little was I prepared for the montrosity that was Milon Z...
One thing I've learned is that Milon Z's battle script relies 100% on Cecil, or magic being used on him, of course I didn't figure this out until much later... I tried a traditional battle formation at first, Cecil going all out with PowerDrinks, Tellah and Porom on healing, once he started on his Weak chain, I was as good as dead, I must have lost to him at least a dozen times, before I made any significant progress.
I realized that Cecil took significantly more damage when Cursed, and he dealt 1 damage (from his normal PowerDrink 100-300). I set up a network that would keep him healed at all times, 5 Remedies and 3 Crosses... talk about unprepared... after these 8 were gone, and Milon was dealing as much to Cursed Cecil then Cecil was even doing, I quickly started to dry up my inventory of Ethers used to heal him with Esuna on Tellah (Porom didn't know it yet) and I thought I had made good headway, he was no longer countering with Pollen and Weak by this point, everything eventually dried up and Cecil died cursed, so I felt no reason to revive him, then I thought to throw on the White Arrows, and it did significant damage, especially considering the wielder was Cursed.
So I had my strategy, let Cecil die, most of the HP Milon Z restores is because of a cursed Cecil, take away his fountain and watch as he withers and dies. Palom was on the Crossbow and White Arrows, because Porom and Tellah were healbots for the most part. Though one thing that I figured out during my failure of my last attempt was that Blink is much more useful and cost efficient then wasting it on Esuna's. So Porom was nearly always protected from Milon's physical attack dealing Cursed and Poison, throwing on a PowerDrink on Palom had him dealing 300-500 damage a hit to Milon Z, it still took a bit of time (how much HP does he have?!) but he Finally went down. What a fight and what a way required to beat him, I am glad to say I did not go back to grind during any of my failures. Cecil finished his tenure as a Dark Knight at Level 25.
The Dark Knight wasn't... much, really. He was there and he went down after a bit of healing, but given your options, that comes as little surprise (though as a boy, I thought healing the Dark Knight actually sped up the end of the fight, that might be an interesting condition, though perhaps impossible to set).
At this point, I'm going to take a break and try to incorporate your hack changes with my own little remodeling project. It's been a lot of fun!