1. At what point in the game does it refer to the Limit items as "manuals"? I think they're more a significant item to boost their Limit level, and they already know their final attack. The item just allows the capacity to use it.
2. I think I've constructed a little bitty.
Cid's Highwind attack is definitely an overextended and cumulative version of Matra Magic, which is an E. Skill. Obviously, (despite my earlier denial) it does make sense if only because Matra Magic is present in the game.
Cid's Dynamite attack is also strange, but I think I understand it now. The question of where the weapon comes from is how the spirit energy ties in. I believe in this case it's like Fullmetal Alchemist. His spirit energy makes him a Dragoon/Alchemist and he merely transmutes available items into Dynamite.
Barret's Satellite Beam, imo, really is connected to a satellite, but by no normal means could Barret contact the satellite to fire on his enemies. I believe the spirit energy is what allows him to communicate with, at least, the satellite.