To update your mod to version 1.001, you need to make a few changes to your rulesmd.ini and soundmd.ini files.
The changes you need to make are listed below.

rulesmd.ini changes:

= modified flag/section
= new flag/section
= this change gets reverted in 1.002 so you can just ignore it here.

[GHOST]
CreateSound=SealCreated

[YURIPR]
ImmuneToPsionicWeapons=yes ;gs Patch

[CLNT]
UIName=Name:Hero1
Name=Cowboy
VoiceSelect=GISelect
VoiceMove=GIMove
VoiceAttack=GIAttackCommand
VoiceFeedback=GIFear
VoiceSpecialAttack=GIMove
DieSound=GIDie

[ARND]
UIName=Name:Hero3
Name=Hero
VoiceSelect=GISelect
VoiceMove=GIMove
VoiceAttack=GIAttackCommand
VoiceFeedback=GIFear
VoiceSpecialAttack=GIMove
DieSound=GIDie

[STLN]
UIName=Name:Hero2
Name=Bodybuilder
VoiceSelect=GISelect
VoiceMove=GIMove
VoiceAttack=GIAttackCommand
VoiceFeedback=GIFear
VoiceSpecialAttack=GIMove
DieSound=GIDie

[HTNK]
BuildTimeMultiplier=1.3

[APOC]
BuildTimeMultiplier=1.0

[TTNK]
BuildTimeMultiplier=1.2

[CAOS]
Strength=130
Cost=1000
Soylent=1000
BuildTimeMultiplier=1.1

[SMIN]
Cost=1750
Soylent=1750
BuildTimeMultiplier=0.8

[SCHP]
Cost=1100
Soylent=1100
VoiceSecondaryWeaponAttack=SeigeChopperAttackLand

[BPLN]
Strength=200

[SPYP]
Strength=600

[YAREFN]
Cost=1750
Soylent=1750
BuildTimeMultiplier=1.15

[CALA05]
CanOccupyFire=yes

[AGGattling]
Range=6

[AGGattling2]
Range=6

[AGGattling3]
Range=6

[ChaosAttack]
ROF=45

[AGGattlingE]
Range=6

[AGGattling2E]
Range=6

[AGGattling3E]
Range=6

[MagneticBeamE]
Range=12

[GUARDWH]
CellSpread=.5;gs patch
PercentAtMax=.5;gs patch

[PsiPulse]
AffectsAllies=no;gs Patch Defaults to yes.

 

soundmd.ini changes:

= modified flag/section
= new flag/section

[SoundList]
855=SealCreated

[SealSelect] 
Sounds= $iseaseb $iseased $iseaexc

[SealCreated]
Sounds= $iseasea
Priority=CRITICAL
Type=Global
MinVolume=90
Volume=90