Aw hell, you got a HP Plus? Did you get it from a shop or from the Junon harbour send-off? I was trying to keep Plus Materia in the Crater and specced story bosses for a non-Plus team. Looks like I've missed a vendor somewhere.
Balancing enemies gets tough from around the Icicle area and onwards because that's roughly where differences in play-style hit a point where it's tough to accommodate everyone; there's roughly three kinds of players: people who only fight what they run into, people who grind up for things like Lv.3 Limit Breaks, and 'rush' players who run from most random encounters. It's about that area where I think the widening gulf between these three types reaches a critical point and it gets worse from there on. If you spec up to handle the heavy grind players, everyone below that suffers as a result. I was aiming for that mid-range with the old version of the mod but I miscalculated; it's perhaps made me too cautious but better they're too weak than too strong. I'll test them out with a 'low' team and push their stats/attacks a little bit if they're still lacking firepower.
I don't think there's any Scorpion encounter between Dyne and the Junon escape from what I can remember. There were, counting the two in Reactor No.1, seven encounters with it in all although Fight No. 6 is technically optional.
The Materia like Full-Cure (which now has an Esuna affect attached to it), W-Item, etc. are all being kept either in the Crater or as prizes in the Extra Battle. Once you've beaten a monster from the EB roster, talking to the middle NPC will have him check for which monsters are dead and he'll dispense the Materia associated with them. Comet should be tied up with the Corel Train scenario but failing it means having the find Comet elsewhere.
Morph is being kept by the Kalm Traveller for when you get all three items for him; I set up an area for each source, so every enemy in Mythril Mines for instance will morph into a Guard Source (although I imagine if stat-maxing is going to happen it'll be done through Black Chocobo but I figured it'd be an idea to have a way of doing it easily in-game).
For Cloud, Tifa, and Cid, make sure to have them as party leader when going for their Lv.4/Ult.