A slight update, when I was looking at some data yesterday I seemed to have come across what goes on when you use a command. Curiously enough both 0D (Focus/Power) and 06 (Jump) are only "half" of commands.
Here's what my data managed to find...
(Address markers found in Cheat Engine so clearly, not the real address in a debugger)
0x72D4B8 - Atttack Algorithm?
80 0D 00 40 00 06 (When charging Focus Attack)
80 1F 00 20 00 06 (Focus Attack)
Yet if you happen to put 1F onto your command menu you will not have the double damage that comes from the normal use of Focus/Power, the same applies with Jump. This leads me to wonder, since the Command is quite literally linking to another Command, is it possible to change that which will be given the x2 attack? Say you wanted to make a double damage Dark Wave, that only downside is the charge time of Focus. But where this data comes into play is a bit beyond me. Perhaps some tracing could help, but tracing anything with ZSNES is laborious enough.