I realized that there was a line calling for an animation that is part of the super form animations that was causing some of the trouble, as it isn't in the animation file I made. However, after correcting that I still couldn't get all animations to load.
SonicAniData:
dc.w SonAni_Walk - SonicAniData ; 0
dc.w SonAni_Run - SonicAniData ; 1
dc.w SonAni_Roll - SonicAniData ; 2
dc.w SonAni_Roll2 - SonicAniData ; 3
dc.w SonAni_Push - SonicAniData ; 4
dc.w SonAni_Wait - SonicAniData ; 5
dc.w SonAni_Balance - SonicAniData ; 6
dc.w SonAni_LookUp - SonicAniData ; 7
dc.w SonAni_Duck - SonicAniData ; 8
dc.w SonAni_Spindash - SonicAniData ; 9
dc.w SonAni_Blink - SonicAniData ; 10 ; $A
dc.w SonAni_GetUp - SonicAniData ; 11 ; $B
dc.w SonAni_Balance2 - SonicAniData ; 12 ; $C
dc.w SonAni_Stop - SonicAniData ; 13 ; $D
dc.w SonAni_Float - SonicAniData ; 14 ; $E
dc.w SonAni_Float2 - SonicAniData ; 15 ; $F
dc.w SonAni_Spring - SonicAniData ; 16 ; $10
dc.w SonAni_Hang - SonicAniData ; 17 ; $11
dc.w SonAni_Dash2 - SonicAniData ; 18 ; $12
dc.w SonAni_Dash3 - SonicAniData ; 19 ; $13
dc.w SonAni_Hang2 - SonicAniData ; 20 ; $14
dc.w SonAni_Bubble - SonicAniData ; 21 ; $15
dc.w SonAni_DeathBW - SonicAniData ; 22 ; $16
dc.w SonAni_Drown - SonicAniData ; 23 ; $17
dc.w SonAni_Death - SonicAniData ; 24 ; $18
dc.w SonAni_Hurt - SonicAniData ; 25 ; $19
dc.w SonAni_Hurt - SonicAniData ; 26 ; $1A
dc.w SonAni_Slide - SonicAniData ; 27 ; $1B
dc.w SonAni_Blank - SonicAniData ; 28 ; $1C
dc.w SonAni_Balance3 - SonicAniData ; 29 ; $1D
dc.w SonAni_Balance4 - SonicAniData ; 30 ; $1E
dc.w SupSonAni_Transform - SonicAniData ; 31 ; $1F
dc.w SonAni_Lying - SonicAniData ; 32 ; $20
dc.w SonAni_LieDown - SonicAniData ; 33 ; $21
dc.w SonAni_Peel - SonicAniData ; 34 ; $22
dc.w SonAni_PeelCharge - SonicAniData ; 35 ; $23
dc.w SonAni_PeelCharge2 - SonicAniData ; 36 ; $24
dc.w SonAni_dash - SonicAniData ; 37 ; $25
dc.w SonAni_pose - SonicAniData ; 38 ; $26
dc.w SonAni_spindashcharge - SonicAniData ; $27
dc.w SonAni_spindashcharge2 - SonicAniData ; $28
dc.w SonAni_jumpdash - SonicAniData ; $29
dc.w SonAni_jump - SonicAniData ; $2A ???
dc.w SonAni_Wallgrab - SonicAniData ; 2B
dc.w SonAni_Duck2 - SonicAniData ; 2C
dc.w SonAni_SpindashRev - SonicAniData ; 2D
dc.w SonAni_stompfall - SonicAniData
dc.w SonAni_Stand - SonicAniData
SonAni_Walk: dc.b $FF, $C,$D,$E,$F,$10,$11, $12, $13,$FF
SonAni_Run: dc.b $FF,$2C,$2D,$2E,$2F,$FF,$FF,$FF,$FF,$FF
SonAni_Roll: dc.b $FE,$3C,$40,$3D,$40,$3E,$40,$3F,$40,$FF
SonAni_Roll2: dc.b $FE,$3C,$40,$3D,$40,$3E,$40,$3F,$40,$FF
SonAni_Push: dc.b $FD,$48,$49,$4A,$4B,$FF,$FF,$FF,$FF,$FF
SonAni_Wait:
dc.b 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
dc.b 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2
dc.b 3, 3, 3, 3, 3, 4, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5
dc.b 5, 4, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 6, 6, 6
dc.b 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 5, 5, 5, 4, 4, 4
dc.b 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 6
dc.b 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 5, 5, 5, 4
dc.b 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5
dc.b 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 5, 5
dc.b 5, 4, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 4, 4
dc.b 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 8, 8
dc.b 8, 9, 9, 9,$FE, 6
SonAni_Balance: dc.b 9,$CC,$CD,$CE,$CD,$FF
SonAni_LookUp: dc.b 5,$B,$FE, 1 ; 5, $B, $C,$FE, 1
SonAni_Duck: dc.b 5,$4C,$FE, 1
SonAni_Spindash:dc.b 7,$41,$42,$43,$44,$FF ; new spindash animation, uses 2 less frames than the original, and unlike the original does not use a frame between each
SonAni_Blink: dc.b 1, 2,$FD, 0
SonAni_GetUp: dc.b 3, $A,$FD, 0
SonAni_Balance2:dc.b 3,$C8,$C9,$CA,$CB,$FF
SonAni_Stop: dc.b 5,$D1,$D2,$D3,$D4,$FD, 0 ; halt/skidding animation
SonAni_Float: dc.b 7,$54,$59,$FF
SonAni_Float2: dc.b 7,$54,$55,$56,$57,$58,$FF
SonAni_Spring: dc.b $2F,$5A,$FD, 2
SonAni_Hang: dc.b 1,$50,$51,$FF
SonAni_Dash2: dc.b $F,$43,$43,$43,$FE, 1
SonAni_Dash3: dc.b $F,$43,$44,$FE, 1
SonAni_Hang2: dc.b $13,$6B,$6C,$FF
SonAni_Bubble: dc.b $B,$5A,$5A,$11,$12,$FD, 0 ; breathe
SonAni_DeathBW: dc.b $20,$5E,$FF
SonAni_Drown: dc.b $20,$5D,$FF
SonAni_Death: dc.b $20,$5B,$FF
SonAni_Hurt: dc.b $40,$4E,$FF
SonAni_Slide: dc.b 9,$4E,$4F,$FF
SonAni_Blank: dc.b $77, 0,$FD, 0
SonAni_Balance3: dc.b $13,$D0,$D1,$FF
SonAni_Balance4: dc.b 3,$CF,$C8,$C9,$CA,$CB,$FE, 4
SonAni_Lying: dc.b 9, 8, 9,$FF
SonAni_LieDown: dc.b 3, 7,$FD, 0
SonAni_Peel: dc.b $FF,$D7,$D8,$D9,$DA,$D7,$D8,$D9,$DA,$FF
SonAni_PeelCharge: dc.b 2, $E,$F,$10,$11,$2C,$2D,$2E,$2F,$FD,$24 ;3
SonAni_PeelCharge2:dc.b 0,$D6,$D7,$D8,$D9,$D6,$D7,$D6,$D9,$FF
SonAni_dash: dc.b $20, $E7, $FD, 2
Sonani_pose: dc.b 0,$5D,$FF
SonAni_spindashcharge: dc.b 5,$3C,$40,$3D,$40,$3E,$40,$3F,$40,$FD,$28
SonAni_spindashcharge2: dc.b 0,$3C,$40,$3D,$40,$3E,$40,$3F,$40,$FF
SonAni_jumpdash: dc.b 0,$E7,$E8,$FD,2
SonAni_jump: dc.b $FE,$3C,$40,$3D,$40,$3E,$40,$3F,$40,$FF
SonAni_Wallgrab: dc.b 0,$4B,$FF
SonAni_Duck2: dc.b $2F,$4C,$FD, 0
SonAni_SpindashRev: dc.b 7,$E9,$EA,$EB,$EC,$FD, 9
SonAni_stompfall: dc.b $2,$4C,$FD, $2F
SonAni_Stand: dc.b 0, $1,$FF
even
SuperSonicAniData:
dc.w SupSonAni_Walk - SuperSonicAniData ; 0
dc.w SupSonAni_Run - SuperSonicAniData ; 1
dc.w SonAni_Roll - SuperSonicAniData ; 2
dc.w SonAni_Roll2 - SuperSonicAniData ; 3
dc.w SupSonAni_Push - SuperSonicAniData ; 4
dc.w SupSonAni_Stand - SuperSonicAniData ; 5
dc.w SupSonAni_Balance - SuperSonicAniData ; 6
dc.w SonAni_LookUp - SuperSonicAniData ; 7
dc.w SupSonAni_Duck - SuperSonicAniData ; 8
dc.w SonAni_Spindash - SuperSonicAniData ; 9
dc.w SonAni_Blink - SuperSonicAniData ; 10 ; $A
dc.w SonAni_GetUp - SuperSonicAniData ; 11 ; $B
dc.w SonAni_Balance2 - SuperSonicAniData ; 12 ; $C
dc.w SonAni_Stop - SuperSonicAniData ; 13 ; $D
dc.w SonAni_Float - SuperSonicAniData ; 14 ; $E
dc.w SonAni_Float2 - SuperSonicAniData ; 15 ; $F
dc.w SonAni_Spring - SuperSonicAniData ; 16 ; $10
dc.w SonAni_Hang - SuperSonicAniData ; 17 ; $11
dc.w SonAni_Dash2 - SuperSonicAniData ; 18 ; $12
dc.w SonAni_Dash3 - SuperSonicAniData ; 19 ; $13
dc.w SonAni_Hang2 - SuperSonicAniData ; 20 ; $14
dc.w SonAni_Bubble - SuperSonicAniData ; 21 ; $15
dc.w SonAni_DeathBW - SuperSonicAniData ; 22 ; $16
dc.w SonAni_Drown - SuperSonicAniData ; 23 ; $17
dc.w SonAni_Death - SuperSonicAniData ; 24 ; $18
dc.w SonAni_Hurt - SuperSonicAniData ; 25 ; $19
dc.w SonAni_Hurt - SuperSonicAniData ; 26 ; $1A
dc.w SonAni_Slide - SuperSonicAniData ; 27 ; $1B
dc.w SonAni_Blank - SuperSonicAniData ; 28 ; $1C
dc.w SonAni_Balance3 - SuperSonicAniData ; 29 ; $1D
dc.w SonAni_Balance4 - SuperSonicAniData ; 30 ; $1E
dc.w SupSonAni_Transform - SuperSonicAniData ; 31 ; $1F
dc.w SupSonAni_Peel - SuperSonicAniData ; 32 ; 20
dc.w SupSonAni_PeelCharge - SuperSonicAniData ; 33 ; 21
dc.w SupSonAni_PeelCharge2 - SuperSonicAniData ; 34 ; 22
SupSonAni_Walk: dc.b $FF,$77,$78,$79,$7A,$7B,$7C,$75,$76,$FF
SupSonAni_Run: dc.b $FF,$B5,$B9,$FF,$FF,$FF,$FF,$FF,$FF,$FF
SupSonAni_Push: dc.b $FD,$BD,$BE,$BF,$C0,$FF,$FF,$FF,$FF,$FF
SupSonAni_Stand: dc.b 7,$72,$73,$72,$73,$FF
SupSonAni_Balance: dc.b 9,$C2,$C3,$C4,$C3,$C5,$C6,$C7,$C6,$FF
SupSonAni_Duck: dc.b 5,$C1,$FF
SupSonAni_Transform: dc.b 2,$6D,$6D,$6E,$6E,$6F,$70,$71,$70,$71,$70,$71,$70,$71,$FD, 0
SupSonAni_Peel: dc.b $FF,$B5,$B9,$B5,$B9,$B5,$B9,$B5,$B9,$FF
SupSonAni_PeelCharge: dc.b 2, $F,$77,$78,$79,$B5,$B9,$B5,$B9,$FD,$22 ;3
SupSonAni_PeelCharge2: dc.b 0,$B5,$B9,$B5,$B9,$B5,$B9,$B5,$B9,$FF
even
That is the animation file, now however this is what I get in SonAni2Gif: