Hmm...

You shouldn't need to customise Triple AP yourself. Even if you do want to, you don't need Dark Matters to do that, you need Wings to Discovery. Anyway, a much easier way to get Triple AP weapons is to fight the One-Eye (under Species Creations), that should drop them. The person who gets the final attack in the battle is the most likely to get the weapon, although that's not a given.

As for Dark Matters, yes you get 99 when Ultima Buster is created, but they can also be dropped by any of the arena creations after battle. It's rare though, so you may be fighting a while if you want some more.