So, I just finished the mod and, once again, I must say that it truly is an amazing piece of work. I had a great time with it and loved almost all of it.
Here are some more things I found:
1) The check for finishing a playthrough without using up any SP seems glitched. I ranked up all my characters but was still told by Mr. Smiles that I had not used up any sources.
2) The Stardust Item is severely overpowered. 24,000 HP of damage to any single target regardless of its defense is quite game-breaking, in particular since most enemies have fairly little HP by other mods' standards.
3) Some materia equip penalties seem too harsh. For instance, the -26 MDef granted by several support materia makes those materia very unattractive to use.
4) Some pieces of armor seem nerfed into uselessness. Whereas the Mystile and Ziedrich are the go-to late game pieces of armor in vanilla, in New Threat Mod, I never found myself using them because they offer no Def or MDef in addition to ulterior penalties (no Resist/Shield status as well as unlinked slots in the case of the Mystile). Instead, I ended up using the Imperial Guard or Dragon Armlet, which seem to be by far the the most well-rounded pieces of armor post-game. On a similar note, I actually found the Relic Ring quite interesting, however, the benefit conferred by it is clearly outmatched by its huge downside of causing death by Elixirs. It seems to me that a much larger upside would be required to render this accessory more appealing. The Curse Ring, on the other hand, seems much more usable even though it is subject to a similar handicap. Then again, the Curse Ring is mainly only usable because of how Recovery overrides nullification from an element in FF7's game mechanics. If the Curse Ring did not nullify but also absorb Health, just like the Relic Ring does, that would make it much trickier to use.
5) The scene.bin contains lots of enemies that one cannot fight. Is that correct or did I just not find a way to do so? For instance, what about the enemy from which one could get the Magitek Ashes item? I could not find a scene that triggers a fight with that enemy.
6) One of the two Long Range materia one acquires via the Kalm Traveller sidequest has its AP not set to Master, which is not much of an issue unless one finds oneself in the unfortunate position of suffering from above-average OCD.
7) Generally speaking, the difficulty Level on Arrange was more than just fair. I had finished a playthrough of Gjoerulv's Hardcore Mod just prior to my most recent playthrough of your New Threat Mod and it seems that I had a much easier time beating all the enemies in your mod than in Gjoerulv's one. That's not necessarily a bad thing or only a quality inherent to your mod, however, the differential in difficulty really did strike me. For instance, random encounters in the Northern Crater are preferably completely avoided in the Hardcore Mod, while one can comfortably use them to level up in the New Threat Mod. The optional bosses in New Threat Mod could all stand to become a bit more challenging. On an anecdotal note, I did not want to spend any time breeding a Gold Chocobo, even with the no-racing-required method, and not having realized that the Guide Book instead of the Desert Rose yields the Gold Chocobo in NTM, I set out to beat Ruby/Viridian Weapon because I wagered that it would take me much less time than doing the Chocobo breeding and I was not proven wrong. To be fair though, I did like the fact that the NTM version of Ruby Weapon is much less annoying to fight (no sky-high defensive stats and no need to set up the fight with two dead characters). Still, it appeared to me that the primarily the brevity of the fight, since the enemy had less than 300K HP, made it almost too easy for my taste.
8 ) Doubling all characters' Def and MDef via AI is somewhat game-breaking once one can attain 255 in either (made more feasible by means of HP<->MP Materia) and even more so once can attain 255 in both stats with a single character. All damage from attacks that do no use special damage formulas becomes negligible. I wonder if that was the intended way to beat FF X Nemesis in the battle arena.
9) I thoroughly enjoyed the whole Fort Condor quest obsession. ;] It was a very nice surprise to get something useful out of it at the very end.