The code you provided for the relics, zeemis, will only change commands in the menu - the bank C3 deals with all matters in the menu.
If you want any changes to apply in battle as well, you need to go over the C2 bank.
Code:
C2/53A5: B9 FC 00 LDA $00FC,Y (get command from menu slot)
C2/53A8: A2 04 LDX #$04
C2/53AA: 48 PHA
C2/53AB: A9 04 LDA #$04
C2/53AD: 85 EE STA $EE (start checking Bit 2 of variable $11D6)
C2/53AF: BF 52 54 C2 LDA $C25452,X (commands that can be changed FROM)
C2/53B3: C3 01 CMP $01,S (is current command one of those commands?)
C2/53B5: D0 0D BNE $53C4 (branch if not)
C2/53B7: AD D6 11 LDA $11D6 (check Battle Effects 1 byte.
Bit 2 = Fight -> Jump, Bit 3 = Magic -> X-Magic,
Bit 4 = Sketch -> Control, Bit 5 = Slot -> GP Rain,
Bit 6 = Steal -> Capture)
C2/53BA: 24 EE BIT $EE
C2/53BC: F0 06 BEQ $53C4
C2/53BE: BF 57 54 C2 LDA $C25457,X (commands to change TO)
C2/53C2: 83 01 STA $01,S (replace command on stack)
C2/53C4: 06 EE ASL $EE (will check the next highest bit of $11D6
in our next iteration)
C2/53C6: CA DEX
C2/53C7: 10 E6 BPL $53AF (loop for all 5 possible commands that can be
converted)
The two important parts of code are as follows:
C2/53AF: BF 52 54 C2 LDA $C25452,X (commands that can be changed FROM) ***LOADS ADDRESS C2/5452, which contains the commands
Code:
(Data - commands that can be replaced with other commands thanks to Relics)
C2/5452: 05 (Steal)
C2/5453: 0F (Slot)
C2/5454: 0D (Sketch)
C2/5455: 02 (Magic)
C2/5456: 00 (Fight)
The second important part of the code is the one that loads the new command:
C2/53BE: BF 57 54 C2 LDA $C25457,X (commands to change TO) ***LOADS ADDRESS C2/5457
Code:
(Data - commands that can replace above commands due to Relics)
C2/5457: 06 (Capture)
C2/5458: 18 (GP Rain)
C2/5459: 0E (Control)
C2/545A: 17 (X-Magic)
C2/545B: 16 (Jump)
I may be missing something, but that's all I could find concerning the swapping of commands done by relics. Hope this helps :p
Good deal, thanks. Me and Djinn were looking over this today via Skype.