Thanks, bud. Glad you've enjoyed it so far though I agree with you that it could use some tweaking. Thing is, the gap between different play-styles (limit break grinders, fight what you see, and run from everything) gets bigger and bigger as the game goes on and while I thought that 2x Exp, Ap, and Gil would help people close that gap if they found themselves underpowered later on it actually made the problem worse on the other end; the guys grinding for their Lv.3 Limits ended up being super-powered and players taking a 'fight what I run into' approach were also finding themselves ahead of the arc because of the boosted rewards. I'm thinking of maybe turning it down to 1.5 for Exp, and normal for AP but not sure yet.
About Sephiroth in the Whirlwind Maze, the first form was originally a lot tougher but people were saying that it was too much to get through that + the second boss right after it (which was also a lot tougher). So I toned that particular boss fight down a fair bit. That's been the case for a lot of it; just toning down the random fights and some of the bosses (people were save-editing past the bosses in v1.0.5). But I was thinking of maybe adding the option for a Hard Mode; I can re-spec enemies and 'unlock' new attacks by setting a pre-battle AI that checks for a certain variable. That might be a solution, or a NewGame+ kind of deal with new sidequests/encounters, etc. unlocking on the second playthrough; Kalderasha has been giving me ideas recently.
About the triple-AP weapons, did you start from a pre-existing save-game (like starting from the save point in Reactor 1 to skip the intro) or a New Game? The initial set-up of characters from the game's kernel is determined on a New Game rather than when that character joins the party. It just seems odd they'd have their original starting weapons equipped; I've had their weapons set to Metal Knuckle and Full Metal Staff in the mod's kernel for a while now. Did Aeris join the party with Barrier (Lv.2) + All, Heal, and Revive Materia? Another thing is that Red XIII was supposed to have Earth + Elemental on top of Fire + All; do you remember if he had that equipped when he joined the party?
One thing I'm wondering about though is when you say the Sephiroth battle makes you use all the neglected party members. As far as I'm aware, the game should only make you have Cloud and Tifa in your party for the Whirlwind Maze. Has a third character been locked into your party?