Those are all excellent questions! And the vast majority I have found the answer to.
Changing the spells cast by Twin is a very simple matter. You may even change the chance of failure. (It would change the instruction) and if so desired change That to cast a Third Spell instead of the "Failure" message. In reality its easier to cast Spells than it is to display Messages.
Changing messages is also rather simple, but will likely require a fine tooth comb to find and place each one through the fairly extensive notes. They can be turned off by disabling the command, yes.
You can change the status given by Jump and Charge, but both of their adjoining routines on completion get rid of the afflicted status of Jump and Charge. You could change it to something else, but that still wouldn't prevent the graphic for "Jump" from showing up.
Now equipment ranges for commands were found a long time ago and yes, it is easy to turn it off completely.
Charge doesn't actually boost a Stat. What Charge does is simply applies the status of Charge. There is something in the Fight Routine which looks to see if Charge is on the character and if it is to double the damage dealt (this is also the same routine for Jump as well) While you can change this. It won't do much to change what the Charge routine does... which is apply Charge.
In addition is who is set to Hide. We have the check for Paladin Cover, so it seemed also a good idea to put Auto-Hide as well.
In ROM at... Non-headered
Auto-Hide0x1A607 - C9 05 (Character ID of the character that, if they happen to have Auto-Hide, will auto-hide even when their menu is shown)
0x1AD56 - C9 05 (Character ID of the character that will Hide of its own volition when in Critical)
0x1AF0B - A9 09 (The Command the Character who ordinarily Hides will perform on themselves)
Command Conditions and Equip RangesThe possibilities are immense! Do you want to make magic require a Staff or Rod equipped? Or for Dark Wave to actually require a Dark Sword? How about a Whip to use Call, or Two Handed Weapon for Jump?
While there are plenty of possibilities, there's only three that can be utilized. You may change Dark Wave's limits to another command and restrict (or expand?) the range of which it can be used (In example, Require Rosa to use a Staff to use a (better?) Pray.)
And the same applies for the other commands! This opens up a lot for me and I hope it helps you all as well!
In ROM this is located at...
01A48E - C9 05 (Compare with Dark Wave's Command)
01A492 - C9 08 (Compare with Sing's Command)
01A496 - C9 0C (Compare with Aim's Command)
01A49A - C9 10 (Compare with Twin's Command)
01A4F8 - C9 61 (Right Handed - If the Weapon value is this or above this (or 00?) Dark Wave cannot be used)
01A504 - C9 61 (Left Handed - If the Weapon value is this or above this (or 00?) Dark Wave cannot be used (May be Equipped Hand)
01A50E - C9 44 (Right Handed - If the value is this or above this, Sing can be used)
01A512 - C9 4D (Right Handed - If the value is this or above this, Sing cannot be used)
01A51C - C9 44 (Left Handed - If the value is this or above this, Sing can be used)
01A520 - C9 4D (Left Handed - If the value is this or above this Sing cannot be used)
01A52A - C9 54 ( - If the value is this or above this Aim can be used.
01A52E - C9 61 (Right Handed - If the values it this or above this Aim cannot be used (Looking for Bow? This would hint that Aim can be used with two Arrows equipped or two bows... well I'll give it a shot... Yep. Looks like it's right. Aim can be used with Two Bows or Two Arrows. An interesting non-check. Good on the programmers.)

2 -
I've taken another look about the surrounding data and I noticed an interesting pattern...
03A2F3 - BD 33 20 (7E2033 the location of the character's Right Hand Weapon)
03A2F6 - F0 07 (???)
03A2F8 - C9 61 (Right Handed Dark Wave Ranges)
Twincast Probabilities...It might be best to use WindHex and then change it's Displayed Offset to SNES LoRom. for these.
Golbez-FuSoYa TwincastRAM
$03/E56E BD
00 20 LDA $2000,x[$7E:2080] A:0000 X:0080 Y:0005 P:envMxdiZc -
Load Character 1's Character ID into A.
$03/E571 29 1F AND #$1F A:0089 X:0080 Y:0005 P:eNvMxdizc - -80 to A
$03/E573 C9
13 CMP #$13 A:0009 X:0080 Y:0005 P:envMxdizc - Is it
FuSoYa?
$03/E575 F0 04 BEQ $04 [$E57B] A:0009 X:0080 Y:0005 P:eNvMxdizc - If so branch to 03E57B.
$03/E577 C9
15 CMP #$15 A:0009 X:0080 Y:0005 P:eNvMxdizc - Is it
Golbez?
$03/E579 D0 04 BNE $04 [$E57F] A:0009 X:0080 Y:0005 P:eNvMxdizc - If not branch to 03E57F.
-----------------------------------------------------------------------------------------------------------------------------------------------------------
$03/E57B A9
5E LDA #$5E A:0015 X:0080 Y:0005 P:envMxdiZC -
Load W. Meteo $03/E57D 80 19 BRA $19 [$E598] A:005E X:0080 Y:0005 P:envMxdizC - Branch Always to 03E598.
Twincast 1/255 Failure...03/E57F 20 93 85 JSR $8593 [$03:8593] A:0009 X:0080 Y:0005 P:eNvMxdizc - Jump to Subroutine (where random number seems to be generated)
$03/E582 C9
FF CMP #$FF A:008F X:0011 Y:0005 P:eNvMxdizC - Was it
FF (or higher)?
$03/E584 90 08 BCC $08 [$E58E] A:008F X:0011 Y:0005 P:eNvMxdizc - If not, branch to 03E58E.
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
$03/E586 A9
11 LDA #$11 A:00FF X:0033 Y:0007 P:envMxdiZC- Load x11 into A.
(Failed Message)$03/E588 8D CA 34 STA $34CA [$7E:34CA] A:0011 X:001B Y:0005 P:envMxdizC - Store A in 7E34CA (Battle Message Area)
Twincast Success Probability$03/E58E C9
40 CMP #$40 A:008F X:0011 Y:0005 P:eNvMxdizc - Is it less than
40?
$03/E590 90 04 BCC $04 [$E596] A:008F X:0011 Y:0005 P:envMxdizC - If so, branch to 03E596.
$03/E592 A9 41 LDA #$
41 A:008F X:0011 Y:0005 P:envMxdizC - Load
Flare into A.
$03/E594 80 02 BRA $02 [$E598] A:0041 X:0011 Y:0005 P:envMxdizC - Branch Always to 03E598.
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Otherwise...
$03/E596 A9
40 LDA #$40 A:0024 X:0064 Y:0007 P:eNvMxdizc - Load
CometI hope that made sense, if it doesn't. Please let me know and I'll try to use a normal syntax. I was a little rushed for time at the moment.