I just figured out that JSR $C88B multiplies A*X! Man, this code makes SO much more sense now. Looks like you already knew that, though.
OK, let me see if I'm following so far. I like to have all of my offsets in one place.
battle
$80/C0B9 C5 00 CMP $00 [$00:1E00] A:0067 X:0094 Y:0008 D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0278 VC:093 FC:26 I:00
$80/C0BB 90 04 BCC $04 [$C0C1] A:0067 X:0094 Y:0008 D:1E00 DB:80 S:1FF0 P:eNvmxdIzc HC:0312 VC:093 FC:26 I:00
$80/C0C1 9C 25 11 STZ $1125 [$80:1125] A:0067 X:0094 Y:0008 D:1E00 DB:80 S:1FF0 P:eNvmxdIzc HC:0336 VC:093 FC:26 I:00
$80/C0C4 C5 02 CMP $02 [$00:1E02] A:0067 X:0094 Y:0008 D:1E00 DB:80 S:1FF0 P:eNvmxdIzc HC:0376 VC:093 FC:26 I:00
$80/C0C6 B0 03 BCS $03 [$C0CB] A:0067 X:0094 Y:0008 D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0410 VC:093 FC:26 I:00
get max damage
$80/C0CB AE 21 11 LDX $1121 [$80:1121] A:0067 X:0094 Y:0008 D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0434 VC:093 FC:26 I:00
$80/C0CE 22 CA C4 80 JSL $80C4CA[$80:C4CA] A:0067 X:0008 Y:0008 D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0474 VC:093 FC:26 I:00
$80/C0D2 85 00 STA $00 [$00:1E00] A:0041 X:0000 Y:0008 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0698 VC:097 FC:26 I:00
player defense value
$80/C0D4 AE 23 11 LDX $1123 [$80:1123] A:0041 X:0000 Y:0008 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0732 VC:097 FC:26 I:00
$80/C0D7 22 26 C5 80 JSL $80C526[$80:C526] A:0041 X:0000 Y:0008 D:1E00 DB:80 S:1FF0 P:envmxdIZc HC:0772 VC:097 FC:26 I:00
$80/C0DB 85 02 STA $02 [$00:1E02] A:0041 X:0033 Y:0000 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0704 VC:100 FC:39 I:00
======================================
$80/C526 86 06 STX $06 [$00:1E06] A:0041 X:0000 Y:0008 D:1E00 DB:80 S:1FED P:envmxdIZc HC:0836 VC:097 FC:39 I:00
$80/C528 A4 06 LDY $06 [$00:1E06] A:0041 X:0000 Y:0008 D:1E00 DB:80 S:1FED P:envmxdIZc HC:0876 VC:097 FC:39 I:00
$80/C52A A2 00 00 LDX #$0000 A:0041 X:0000 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIZc HC:0916 VC:097 FC:39 I:00
$80/C52D 20 81 C7 JSR $C781 [$80:C781] A:0041 X:0000 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIZc HC:0946 VC:097 FC:39 I:00
$80/C530 A2 66 00 LDX #$0066 A:0028 X:0056 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0124 VC:098 FC:39 I:00
$80/C533 20 8B C8 JSR $C88B [$80:C88B] A:0028 X:0066 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0160 VC:098 FC:39 I:00
$80/C536 29 00 FF AND #$FF00 A:0FF0 X:0066 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0588 VC:098 FC:39 I:00
$80/C539 EB XBA A:0F00 X:0066 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0624 VC:098 FC:39 I:00
$80/C53A 85 08 STA $08 [$00:1E08] A:000F X:0066 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0660 VC:098 FC:39 I:00
$80/C53C A4 06 LDY $06 [$00:1E06] A:000F X:0066 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0706 VC:098 FC:39 I:00
$80/C53E A2 00 00 LDX #$0000 A:000F X:0066 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIZc HC:0752 VC:098 FC:39 I:00
$80/C541 20 D1 C7 JSR $C7D1 [$80:C7D1] A:000F X:0000 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIZc HC:0788 VC:098 FC:39 I:00
$80/C544 A2 33 00 LDX #$0033 A:0028 X:00A4 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:1330 VC:098 FC:39 I:00
$80/C547 20 8B C8 JSR $C88B [$80:C88B] A:0028 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:1366 VC:098 FC:39 I:00
$80/C54A 29 00 FF AND #$FF00 A:07F8 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0390 VC:099 FC:39 I:00
$80/C54D EB XBA A:0700 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0426 VC:099 FC:39 I:00
$80/C54E 18 CLC A:0007 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0462 VC:099 FC:39 I:00
$80/C54F 65 08 ADC $08 [$00:1E08] A:0007 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0492 VC:099 FC:39 I:00
$80/C551 85 08 STA $08 [$00:1E08] A:0016 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0538 VC:099 FC:39 I:00
$80/C553 A6 06 LDX $06 [$00:1E06] A:0016 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0624 VC:099 FC:39 I:00
$80/C555 20 6A C6 JSR $C66A [$80:C66A] A:0016 X:0000 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIZc HC:0682 VC:099 FC:39 I:00
$80/C558 A2 33 00 LDX #$0033 A:00DC X:00DF Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0032 VC:100 FC:39 I:00
$80/C55B 20 8B C8 JSR $C88B [$80:C88B] A:00DC X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0068 VC:100 FC:39 I:00
$80/C55E 29 00 FF AND #$FF00 A:2BD4 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0456 VC:100 FC:39 I:00
$80/C561 EB XBA A:2B00 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0492 VC:100 FC:39 I:00
$80/C562 18 CLC A:002B X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0528 VC:100 FC:39 I:00
$80/C563 65 08 ADC $08 [$00:1E08] A:002B X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0598 VC:100 FC:39 I:00
$80/C565 6B RTL A:0041 X:0033 Y:0000 D:1E00 DB:80 S:1FED P:envmxdIzc HC:0644 VC:100 FC:39 I:00
=========================================
$80/C0DD AE 23 11 LDX $1123 [$80:1123] A:0041 X:0033 Y:0000 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0750 VC:100 FC:39 I:00
$80/C0E0 A0 0C 00 LDY #$000C A:0041 X:0000 Y:0000 D:1E00 DB:80 S:1FF0 P:envmxdIZc HC:0802 VC:100 FC:39 I:00
$80/C0E3 22 85 C5 80 JSL $80C585[$80:C585] A:0041 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0838 VC:100 FC:39 I:00
base defense -- rooks = $19
$80/C0E7 BF 4F C0 80 LDA $80C04F,x[$80:C04F] A:0000 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIZc HC:0024 VC:101 FC:39 I:00
$80/C0EB A2 33 00 LDX #$0033 A:0080 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0078 VC:101 FC:39 I:00
$80/C0EE 20 8B C8 JSR $C88B [$80:C88B] A:0080 X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0114 VC:101 FC:39 I:00
$80/C0F1 29 00 FF AND #$FF00 A:1980 X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0502 VC:101 FC:39 I:00
$80/C0F4 EB XBA A:1900 X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0102 VC:101 FC:26 I:00
+ armor bonus + level bonus
$80/C0F5 18 CLC A:0019 X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0126 VC:101 FC:26 I:00
$80/C0F6 65 02 ADC $02 [$00:1E02] A:0019 X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0144 VC:101 FC:26 I:00
$80/C0F8 85 02 STA $02 [$00:1E02] A:005A X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0178 VC:101 FC:26 I:00
$80/C0FA A9 FF 00 LDA #$00FF A:005A X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0212 VC:101 FC:26 I:00
$80/C0FD 38 SEC A:00FF X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0236 VC:101 FC:26 I:00
$80/C0FE E5 02 SBC $02 [$00:1E02] A:00FF X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0254 VC:101 FC:26 I:00
~~ damage % amount -- $a5 = 0.64453125 x full damage
$80/C100 AA TAX A:00A5 X:0033 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0288 VC:101 FC:26 I:00
get full damage amount??
$80/C101 A5 00 LDA $00 [$00:1E00] A:00A5 X:00A5 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0306 VC:101 FC:26 I:00
$80/C103 20 A1 C8 JSR $C8A1 [$80:C8A1] A:0041 X:00A5 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzC HC:0340 VC:101 FC:26 I:00
======================================================
$80/C8A1 85 22 STA $22 [$00:1E22] A:0050 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIzC HC:0616 VC:096 FC:26 I:00
$80/C8A3 20 8B C8 JSR $C88B [$80:C88B] A:0050 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIzC HC:0650 VC:096 FC:26 I:00
$80/C8A6 85 24 STA $24 [$00:1E24] A:4150 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIzC HC:1026 VC:096 FC:26 I:00
$80/C8A8 A5 22 LDA $22 [$00:1E22] A:4150 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIzC HC:1060 VC:096 FC:26 I:00
$80/C8AA EB XBA A:0050 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIzC HC:1094 VC:096 FC:26 I:00
$80/C8AB 20 8B C8 JSR $C88B [$80:C88B] A:5000 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:1160 VC:096 FC:26 I:00
$80/C8AE 85 22 STA $22 [$00:1E22] A:0000 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0172 VC:097 FC:26 I:00
$80/C8B0 29 00 FF AND #$FF00 A:0000 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0206 VC:097 FC:26 I:00
$80/C8B3 EB XBA A:0000 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0230 VC:097 FC:26 I:00
$80/C8B4 AA TAX A:0000 X:00D1 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0254 VC:097 FC:26 I:00
$80/C8B5 A5 22 LDA $22 [$00:1E22] A:0000 X:0000 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0272 VC:097 FC:26 I:00
$80/C8B7 29 FF 00 AND #$00FF A:0000 X:0000 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0306 VC:097 FC:26 I:00
$80/C8BA EB XBA A:0000 X:0000 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0330 VC:097 FC:26 I:00
$80/C8BB 18 CLC A:0000 X:0000 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZC HC:0354 VC:097 FC:26 I:00
$80/C8BC 65 24 ADC $24 [$00:1E24] A:0000 X:0000 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIZc HC:0372 VC:097 FC:26 I:00
$80/C8BE 90 01 BCC $01 [$C8C1] A:4150 X:0000 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIzc HC:0406 VC:097 FC:26 I:00
$80/C8C1 60 RTS A:4150 X:0000 Y:0008 D:1E00 DB:80 S:1FEB P:envmxdIzc HC:0430 VC:097 FC:26 I:00
======================================================
final damage
$80/C106 29 00 FF AND #$FF00 A:29E5 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0286 VC:102 FC:26 I:00
$80/C109 85 00 STA $00 [$00:1E00] A:2900 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0310 VC:102 FC:26 I:00
$80/C10B 8A TXA A:2900 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0344 VC:102 FC:26 I:00
$80/C10C 05 00 ORA $00 [$00:1E00] A:0000 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIZc HC:0362 VC:102 FC:26 I:00
$80/C10E EB XBA A:2900 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0396 VC:102 FC:26 I:00
$80/C10F 85 00 STA $00 [$00:1E00] A:0029 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0420 VC:102 FC:26 I:00
$80/C111 AE 21 11 LDX $1121 [$80:1121] A:0029 X:0000 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0454 VC:102 FC:26 I:00
$80/C114 AC 23 11 LDY $1123 [$80:1123] A:0029 X:0008 Y:000C D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0494 VC:102 FC:26 I:00
$80/C117 20 B1 C5 JSR $C5B1 [$80:C5B1] A:0029 X:0008 Y:0000 D:1E00 DB:80 S:1FF0 P:envmxdIZc HC:0534 VC:102 FC:26 I:00
$80/C11A AA TAX A:0002 X:0005 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0538 VC:113 FC:26 I:00
$80/C11B BF 76 C1 80 LDA $80C176,x[$80:C178] A:0002 X:0002 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0596 VC:113 FC:26 I:00
$80/C11F A6 00 LDX $00 [$00:1E00] A:0100 X:0002 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0638 VC:113 FC:26 I:00
$80/C121 22 39 8A 80 JSL $808A39[$80:8A39] A:0100 X:0029 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0672 VC:113 FC:26 I:00
$80/C125 A5 01 LDA $01 [$00:1E01] A:0000 X:0000 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIZc HC:0616 VC:114 FC:26 I:00
$80/C127 85 00 STA $00 [$00:1E00] A:0029 X:0000 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0650 VC:114 FC:26 I:00
$80/C129 AE 21 11 LDX $1121 [$80:1121] A:0029 X:0000 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0684 VC:114 FC:26 I:00
$80/C12C AC 23 11 LDY $1123 [$80:1123] A:0029 X:0008 Y:0003 D:1E00 DB:80 S:1FF0 P:envmxdIzc HC:0724 VC:114 FC:26 I:00
$80/C12F 20 0C C3 JSR $C30C [$80:C30C] A:0029 X:0008 Y:0000 D:1E00 DB:80 S:1FF0 P:envmxdIZc HC:0764 VC:114 FC:26 I:00
So first it makes sure A is between the values at $00 and $02. (BCC/BCS are tricky to remember). Then it looks like $1121 and $1123 are player offsets to load their stats.
-$C4CA loads max damage into $(1E)00.
-$C526 loads the player defense value through several subs.
-->$C781's value is multiplied by #$0066 and divided by 256 (the top byte is taken).
-->$C7D1's value * #$0033 / 256, then added to the total.
-->$C66A's value * #$0033 / 256, then added to the total... which is stored in $02.
(These constants are probably where I could modify how effective the stats are, once I figure out which stat is which.)
Next... I guess we're skipping $C585.
-$C04F,x loads the player's base defense, then * #$0033 / 256.
-This is added into the "player defense value" in $02.
-This modified defense (mDef) is subtracted from FF to get their damage reduction % (DR%).
-Then at $C8A1 it... multiplies the full damage (D) by DR% and stores in $1E24.
-Then it byte-swaps D, multiplies by DR%/256 (stores in X), multiplies by 256, and adds it to the total in $1E24.
...I don't really get what it's doing there, and it looks like some of these traces don't match, but D * DR%/256 should give the reduced damage. After that point I get lost, but I see it going back to referencing the character offsets $1121/1123.
So this is disregarding race/element/buff bonuses (which I expect are multipliers), but it helps to know that damage reduction is largely percentage-based.
EDIT: $C3E1 checks the target's element.
EDIT2:
rainponcho! Your multi-levelup works TOO WELL! This is from killing a Slime in a new game.

(The game soft-locked after this)

For some reason Rooks started with $555F EXP to the next level.