About desperation moves...

I don't know how to solve your problem, but if you trace the code in the desperation attack section, you'll jump where the command is set as magic and enventually end up in the following section. This is where the targeting byte ($11A0) is or is not used:

Code:

C2/274D: 8D 10 34     STA $3410   (Magic and numerous other commands enter here)
C2/2750: 80 02        BRA $2754   (load spell data for [equipment] magic)


C2/2752: A9 EE        LDA #$EE    (select Spell EEh - Battle)
C2/2754: 20 66 29     JSR $2966   (go load spell data)
C2/2757: A5 BB        LDA $BB     (targeting byte as read from $CFFE01 table?)
C2/2759: 1A           INC        
C2/275A: D0 05        BNE $2761   (branch if it wasn't FF.. if it was, it's null, so we use
                                   the spell byte instead)
C2/275C: AD A0 11     LDA $11A0   (spell aiming byte)
C2/275F: 85 BB        STA $BB