This is a really cool Idea. I'm a little hazy (maybe you went into more detail somewhere else?) On the details of exactly which limits you've overcome to the original set of commands.
As I see it, the limits are:
1) bank 03 space (not too difficult to overcome)
2) command name space (pretty sure command names are wedged into a bank of other text data, like character default names &c. This could probably be moved pretty easily, as long as you find all of the pointers into command name data and adjust them appropriately)
3) command ID numbers - probably the toughest to overcome because of how the game regularly adds C0 to the ID for various functions, meaning there can only be a maximum of 3F commands, ever, and we want to make sure to not overwrite things like Change, Parry, Show (well, except in hacks that get rid of Hide), Off, Land (the second half off Jump), the ending portion of Spirit Wave, Running away (I don't think we've ever explored this, but it must be a command), whatever else I might be forgetting...
Welcome back Chillyfeez!
1. Indeed, Bank 03 can be used but then from then on we can link the "which bank to look at" code into a JSR to custom code which looks to see what number the command of Spell Subroutine. As you noted, very easy to deal with.
2. This entire idea came from Command Name space. There is room for 65 (41) more Command names. I've tested this to its logical conclusion.
3. As you noted we are Stuck with 3F commands and nothing will let us go beyond this, because the game uses 00-BF for normal abilities. Anything beyond that is a Command.
I found an old document of Phoenix's which helped me build my original Command Disassembly and I also improved upon what was initially there with notes of my own starting from Jump's Return to a blank at the end. After that it goes back to normal routines. Also yes, that "Run Away" command is normally completely unused. In fact it is so unused no Command ever calls it. You can easily link to it and see its intended effect (I always thought it was meant to act like Morale did in FFI-III where an enemy low enough level or through the Fear spell would run. as you may recall my FFI Spells used this routine with a slight change.) What is odd though is that you still get Exp. as if you killed the foe, which shows they never got as far as they should have when programming it.
1E - A2E9 (03E9A2 - Jump's Return)
1F - 23E8 (03E823 - Focus's Return)
20 - E3E4 (03E4E3 - Spell Casting Portion of Twin)
21 - 4FB3 (03B34F - Wait Command)
22 - 38E4 (03E438 - Something to do with the very end of Regen Routine?)
23 - 0000 (Blank) - ??
23-3F does give us roughly 28 more command slots to work with, which is pretty large, I would say.
Since this may be of some interest to you here are my notes on pointers and all of that business.
Location of Command Pointers
08B850
(Change 03B160 to BF 50 BA 08) - New Location of Command Pointers
(Change 02B201 to BF 00 BB 08) - New Location of Command Stances
(Change 038BB3 to BF 80 BB 08) - New Location of Command Targets
FA850 - Location of Command Names
(Change 03A2AC to BF CC BB 80) - New Location of Status Disabling by Command
As you can guess this is all part of a package, something I'd like to call "Hacker's Paradise" which moves all of the pointers and gives the prospective hackers much more room to fool around with.
Here is what I have done at the moment...
(Change 039FA2 to BF D0 BB 08 ) - New Location of Command Timers
Original Location of Spell Subroutine Pointers (03D2AF) - Change To...
BF 20 BC 08 - New Location of Spell Subroutine Pointers
FFIV-Hacker's Paradise
This patch is designed to Free up a lot of space for potential hackers to use as they will including...
1. 2 new event instructions
A. One new event instruction can cause parts of events to skip if the right flag is on/off, or skip events entirely if a battle was lost.
B. This Event Instruction replaces a chosen Character's Battle Command with another Command.
2. Increase the Command Table from 27 to 3F Allowing for 24 new Command Slots.
3. Increase the Spell Subroutines Table from 34 to 7D that is More than Double the amount of spell Subroutines.
4. Chillyfeez's Shadow Party Hack obviates the purpose of worthless 5x Shadow Slots by instead breaking characters down to their essentials and rebuilding the characters when they rejoin the party since that is done automatically anyhow.
Space to Place Routines (unheadered and 1.1)
0001DE55 - 1195 Bytes!
00023C38-23C80
0023C94- 23FFF (A fair amount of Bytes.)
5FD58 - 680 Bytes!
6E3A0-6F25F EBF (3775 Bytes!)
977F0-97FFF - 80F (2063 Bytes!)
This sort of got me sidetracked from my Side Project as I aimed to make the Side Project have more command space to give enhanced commands to the returning Party Members ala FFIV Advance.