The DGs used to be a case of 'rush one down then rush the other one' but I put the Wall Augur death counter in there to turn things on their head a little. If the player doesn't have Dispel, then it's a case of deciding whether to rush one down and deal with a tougher DG or fight both and then kill them at roughly the same time.
The two back-up fighters are actually part of a mechanic with Jenova WAR's attacks (originally they couldn't be targeted). The boss has an irregular counter-attack called Cell Smash which only targets the two 'allies' behind you. If they die, though, then Cell Smash starts to target your party instead which can get a bit tricky as you're already dealing with two attacks per turn. This makes multi-target spells, Berserk, and certain Limits (Tifa's in particular) risky to use because those two will soak up the damage.
Story-wise, you'd be surprised at how little was needed in the way of editing for Aeris. For the most part only a few lines needed to be re-worded here and there and they're very close to what they originally were. There was one scene that got a more major revision, though, and that was the one in Bugehagen's Observatory just before the return to Forgotten City to use the Ancient Key. In the original game, they basically decide to try and figure out what Aeris was doing but this creates a problem in this mod because she's, well, there. But then I remembered she had these two lines during Cloud's 'dream' just after the Temple segment:
{AERIS}
“The secret is just up here.”
{AERIS}
“At least it should be.
…I feel it.
It feels like I'm being led by something.”
That implies to me that she wasn't sure herself what her plan was, so I played that angle and it more or less solved the problem. As for weapons, she doesn't have any extra but Jenova WAR should have dropped the Fairytale which should cover it. Her only other weapons at that level are the Wizard Staff (re-specced for high level), Princess Guard, and Guard Stick (triple AP).
I think you're the first person who saw the Gil Plus and thought it was a good thing. Most people grumbled about it.
Good to hear it's going well, though; I was Lv.41 when I finished up Disc 2 so you should be alright for levels.