Finally after All of This time I have Located the building blocks of Dark Wave's formula!
I found this in a stupidly simple manner, I breakpointed on the Command Used in the character information in battle and followed it until I came across the answer. It turned out to be not very complicated at all. Let's hope Jump and Focus are as simple...
The two stats that are taken into account are the Physical Attack Multiplier - 001B and Physical Attack Base -
The formula appears to be Physical Attack Multiplier x Physical Attack Base - 25%/50%/75% = Dark Wave's Damage
From the Bab-il Docs here's how to change the formula of Dark Wave to use what you please...

I feared at first that I was just changing the ordinary damage calculation formula, but as this picture would attest the damage formula stayed put.

An asterisk (*) before a description for the data indicates that only records
for characters have or use that type of data (equipment is a good example of
this). Two asterisks (**) before a description for the data indicate that only
monsters have or use that type of data (creature type data, for example).
Three asterisks (***) after a description of the data indicates that the
reader is requested to refer to the monster data document for a more complete
description (again, the creature type data is a good example).
Offset Meaning
------ -------
00 *character id/handedness
bits 0-4: character id
bit 5: unknown
bit 6: left hand equippable
bit 7: right hand equippable
01 *sprite/class
bits 0-3: sprite/class id
bits 4-6: unknown
bit 7: in back row
02 level
03-06 current status anomalies
07-08 current hp
09-0A maximum hp
0B-0C current mp
0D-0E maximum mp
0F *base strength
10 *base agility
11 *base vitality
12 *base wisdom
13 *base willpower
14 *modified strength
15 modified agility
16 *modified vitality
17 black magic power/modified wisdom
18 white magic power/modified willpower
19 attack elemental
1A *attack strong vs. creature types***
1B physical attack multiplier
1C physical attack percent
1D physical attack base
1E attack status 1***
1F attack status 2***
20 elements weak vs***
21 elements very weak vs***
22 magical defense multiplier
23 magical defense percent
24 magical defense base
25 elemental defense (if immunity bit wasn't set)***
26 elemental defense (if immunity bit was set)***
27 *defense strong vs. creature types***
28 physical defense multiplier
29 physical defense percent
2A physical defense base
2B status immunity 1***
2C status immunity 2***
2D-2F unknown
30 *helmet
31 *armor
32 *gauntlet
33 *right hand-item
34 *right hand-quantity
35 *left hand-item
36 *left hand-quantity
37-39 *experience
3A unknown
3B speed modifier. lower = faster. for autobattles, starts at 01;
otherwise starts at 10. slow adds +08, (upper bound 20) haste adds -3
(lower bound 0C)
3C unknown
3D-3F *experience to level up
40 **creature types***
41-50 unknown
51 next command # (from 00 to 1D)
52 next sub-action (item or spell number)
53 next action monster target(s)
54 next action party target(s)
55-5F unknown
60-61 relative speed. equal to (Cecil's agi * 32) / (our agi * 0A). if Cecil
isn't in the batle, an arbitrary character is picked instead. lower
number = faster speed.
62-6F unknown
70 **level and boss bit***
71-72 unknown
73 **item byte***
74-7F unknown
In RAM (LoRom/HiRom) at...
0x03E71B - BD 1B 20 - (LDA 7E201B) - Looks at the value in 201B - Physical Attack Multiplier
0x03E730 - BD 1D 20 - (LDA 7E201D) - Looks at the value in 201D - Physical Attack Base
In ROM at...
0x1E91B - BD 1B 20 - (LDA 7E201B) - Looks at the value in 201B - Physical Attack Multiplier
0x1E930 - BD 1D 20 - (LDA 7E201D) - Looks at the value in 201D - Physical Attack Base
For instance say I wanted to change the Dark Wave into an attack that looked not purely at Physical attributes but instead looked at Wisdom and the Physical Attack Base to deal damage, that way it would remain useful as the Dark Knight continues to increase in level and should they wish for the Paladin to keep it they could allow him to use some Wisdom boosting equipment to keep the attack relevant.
So Chillyfeez looks like you can get your Gil Toss after all! To change and alter the power of Dark Wave is just a matter of knowing the stats and equipment pools of your Dark Wave recipient!
:edit:Fixed a Glaring issue with my addressing (I left the 7 from the initial LoRom/HiRom location)