Final Requests for Help

it gets trickier in that Y needs to be restored for the $3A01 branch.  so you'll want to use the space created by the NOP'ed STA to turn the PLY into relocated twins.

Ah, yep, missed that.
I believe this should fix it:

Code:

C2/399E: A3 05          LDA $05,s
C2/39A0: AA             TAX 
C2/39A1: A9 01          LDA #$01
C2/39A3: 8D 01 34       STA $3401
C2/39A6: E0 08          CPX #$08
C2/39A8: B0 5F          BCS $3A09
C2/39AA: C2 20          REP #$20
C2/39AC: 5A             PHY 
C2/39AD: B9 08 33       LDA $3308,y
C2/39B0: 1A             INC 
C2/39B1: E2 21          SEP #$21
C2/39B3: F0 4B          BEQ $3A00
C2/39B5: EE 01 34       INC $3401
C2/39B8: BD 18 3B       LDA $3B18,x
C2/39BB: 69 32          ADC #$32
C2/39BD: B0 1A          BCS $39D9
C2/39BF: F9 18 3B       SBC $3B18,y
C2/39C2: 90 3C          BCC $3A00
C2/39C4: 30 13          BMI $39D9
C2/39C6: 85 EE          STA $EE
C2/39C8: BD 45 3C       LDA $3C45,x
C2/39CB: 4A             LSR 
C2/39CC: 90 02          BCC $39D0
C2/39CE: 06 EE          ASL $EE
C2/39D0: A9 64          LDA #$64
C2/39D2: 20 65 4B       JSR $4B65
C2/39D5: C5 EE          CMP $EE
C2/39D7: B0 27          BCS $3A00
C2/39D9: 20 5A 4B       JSR $4B5A
C2/39DC: C9 20          CMP #$20
C2/39DE: 90 01          BCC $39E1
C2/39E0: C8             INY 
C2/39E1: B9 08 33       LDA $3308,y
C2/39E4: EA             NOP 
C2/39E5: C9 FF          CMP #$FF
C2/39E7: F0 17          BEQ $3A00
C2/39E9: 8D 35 2F       STA $2F35
C2/39EC: 9D F4 32       STA $32F4,x
C2/39EF: BD 18 30       LDA $3018,x
C2/39F2: 0C 8C 3A       TSB $3A8C
C2/39F5: A9 FF          LDA #$FF
C2/39F7: 99 08 33       STA $3308,y
C2/39FA: EE 01 34       INC $3401
C2/39FD: 7A             PLY 
C2/39FE: 60             RTS 

C2/39FF: EA             NOP 
C2/3A00: 7A             PLY 
C2/3A01: E2 20          SEP #$20
C2/3A03: A9 00          LDA #$00
C2/3A05: 99 48 3D       STA $3D48,y
C2/3A08: 60             RTS 

This should honestly be released as a standalone patch. Do you want to do that, or do you want me to?

Have at it