Hello, here to provide more feedback from my experiences. To give a bit of perspective, I have been grinding a bit more than I ever have during normal gameplay in order to stay "ahead of the curve" because I know the purpose of this mod is to make the game more difficult. I'm not doing Korean MMO-grindfest type gameplay, but I am taking on more random encounters in order to gain AP for important junctions before you traditionally earn them through the course of normal gameplay.
SeeD mission in Dollet: This portion of the game seems well balanced, actually. I will say that running into double Red G-Army soldiers was actually quite threatening, they do a lot of hard damage and aren't pushovers. My characters without HP-Junction were actually killed a few times throughout the mission (importantly, this depleted my supply of Phoenix Down, more on that later). I didn't have any problems with Elvoret or Biggs and Wedge encounters, seemed solid. I tried to kill the X-ATM092 the traditional way, I had stocked up on Lightning Magic but it wasn't nearly enough to kill him.
Timber mission: An important thing I noticed is how few opportunities you have prior to this battle to stock up on items you need in Timber. I did not purchase any Phoenix Downs prior to leaving Balamb, and unless I am mistaken, there is no opportunity to purchase more from a vendor within the city. With two Phoenix Down left and with a party member dead, I had to force the story forward (instead of exploring the city's side quests) in order to use a one-time rest at the inn of the leader of the Forest Fox because the regular inn is not available while the town is under occupation. If I could give a suggestion, I think having the G-Soldiers you encounter while running around town drop Phoenix Downs may alleviate this issue.
Battle vs. the President's body double: Probably the hardest battle I'd encountered so far. Again, I tried to kill him the traditional way a few times but ended up wiping and getting a game over. At this point I became very conscious of the changes you made to character's stats and strengths. I had already noticed that Selphie and Squall are much better at using magic then Zell, but after a few wipes I completely rebalanced my character's magic inventories and Battle abilities via Junction to maximize their effectiveness. I stopped equipping the Magic command and gave Zell the Item command instead; I'd given Selphie the exclusive job of casting our party's strongest heals at Gerogero. I have to say that I am very, VERY pleased with how this aspect of your rebalance is turning out.
Post-Timber: After leaving the train station at West Academy, I instead traveled to Dollet to use the in-game vendors and purchased the Phoenix Downs that I felt that I needed. At this point I decided to do some more AP grinding and unlock Diablos along with the the 3rd HP Junction, which I felt was increasingly necessary. I did wipe to Diablos a few of times, but after some more junction optimization (now getting Rinoa to Stock/Cast Demi because of her advanced Magic stat) I was able to beat him. After getting him to low HP his physical attacks increased in frequency and this is where he was the most dangerous, it seems his speed is a bit high. Overall, I don't have suggestions for this encounter. His difficulty seems reasonable for an optional boss encounter.
The Centra Excavation: I'd gone into Centra without much problem. I was quite upset because I did wipe and lose about 20 minutes worth of progress to a single Elastoid, though. After they go haywire, their spellcast (forgot it's name, sorry) casts for about 800 damage to all party members. Without prior knowledge that this powerful attack would occur, I lost two party members to the first cast and before I could run away or even fill my Laguna's ATB bar, he used the same attack again without me being able to do anything. Lesson learned, maybe I should pay more attention to what the enemies are doing. I did encounter a Gesper and learned about their magic inventory which I took advantage of to get a full stock of Protect and Shell on two characters. I'm not sure whether this is intended, but they present no threat to the party at all. Their single physical attacks inflicts only about 150 damage, and they often attack each other and heal the party. For such a powerful defensive junctioning magic, I think maybe they should be a bit harder to get than through a Gesper that most likely won't kill you.
The final encounter at the Excavation site: I previously used the site's defensive measures to get rid of some of the enemy soldiers that attack you, and that was fortunate for me because this encounter is RIDICULOUSLY HARD. At this point, Kiros had 1000 HP, Laguna had about 1300 HP. Ward had 1500 with 100 Protect and Shell junctioned to physical and magic damage reduction. Despite this, I still died to this about 5 or 6 times total, each time rotating magic and junctions absolutely maximize the amount of damage that my party can take. During the final encounter with the two black-suited Esthar Soldiers, the amount of damage they can do in succession is absolutely ridiculous. I'd often get hit with double Boomerang Sword followed quickly by their physical attack or Aero, which did 400 damage or 800 damage respectively. I only had two options to begin the encounter: try to cast GF as quickly as possible on all of my characters to absorb one of these blows, or hope that I started the encounter with enough ATB to even get off a Protect on any of my characters. I quickly learned that the 2nd option was not really feasible because one or two of my characters would die to the incoming attacks anyway, and the AI was smart enough to start casting Aero against me before I could also cast Shell on anyone/everyone. In the end, the option that worked for me was to use Mega Potions to negate Boomerang Sword damage and heal the entire party as I used others to cast protective spells. Overall I am displeased with this encounter because it is too difficult and because I feel like any chance to beat it is purely RNG dependent. I don't feel like I earned my victory here, despite my efforts to maximize my characters defensive potential at this juncture of the game. I feel like I beat it because I got lucky and the enemy skipped a turn or two.
Overall I am happy to report that I am VERY satisfied with the mod overall though. If I may offer one more important bit of feedback, and this may be an extreme suggestion, but would you consider disabling the GF command in battle? There's not really a lot of strategy to them offensively, they do too much damage to regular monsters and the most efficient option to winning battles is just to cast one and kill everything at once. I'm tired of watching these animations and being so disengaged once they're cast that I'm looking at my phone instead of my screen. I can only think of one strategic use for GFs in battle, which I had to employ against the Esthar soldiers: sacrifice the GF in order to eat an otherwise deadly or disadvantageous attack. I could see this sacrifice being useful later as an intriguing option for early Ultimecia's castle, but otherwise I feel like they are too efficient not to use throughout the game.
Likewise, I don't use Zell in my party any more because his potential damage is so much less than the GF attacks or casted magic that he's pretty useless. I'm not sure how to fix this issue other than maybe making him naturally more tanky than other characters?