[Windows Mobile Software Development] serfer222:
can I suggest to do some code refactoring.

almost all code in the script has its copy, there are always two branches, depending on variable "method" and RegRead( "HKLM", "Comm", "BootCount" ) value. Right?

If (method = 2 )
If (RegRead( "HKLM", "Comm", "BootCount" ) eq 2)
If (FileExists( "\Windows\Cook.mscr" ))
Run("\Windows\Cook.mscr")
Else
EndIf
BattSuspendTimeout = RegRead ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","BattSuspendTimeout")
ACSuspendTimeout = RegRead ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","ACSuspendTimeout")
BatteryTimeout = RegRead ("HKCU", "ControlPanel\Backlight", "BatteryTimeout")
ACTimeout = RegRead ("HKCU", "ControlPanel\Backlight", "ACTimeout")
Brightness = RegRead ("HKCU", "ControlPanel\Backlight", "Brightness")
ACBrightness = RegRead ("HKCU", "ControlPanel\Backlight", "ACBrightness")
RegWriteDword ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","BattSuspendTimeout",0)
RegWriteDword ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","ACSuspendTimeout",0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "BatteryTimeout", 0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "ACTimeout", 0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "Brightness", 10)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "ACBrightness", 10)
Else
EndIf
Else
If (RegRead( "HKLM", "Comm", "BootCount" ) eq 1)
If (FileExists( "\Windows\Cook.mscr" ))
Run("\Windows\Cook.mscr")
Else
EndIf
BattSuspendTimeout = RegRead ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","BattSuspendTimeout")
ACSuspendTimeout = RegRead ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","ACSuspendTimeout")
BatteryTimeout = RegRead ("HKCU", "ControlPanel\Backlight", "BatteryTimeout")
ACTimeout = RegRead ("HKCU", "ControlPanel\Backlight", "ACTimeout")
Brightness = RegRead ("HKCU", "ControlPanel\Backlight", "Brightness")
ACBrightness = RegRead ("HKCU", "ControlPanel\Backlight", "ACBrightness")
RegWriteDword ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","BattSuspendTimeout",0)
RegWriteDword ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","ACSuspendTimeout",0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "BatteryTimeout", 0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "ACTimeout", 0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "Brightness", 10)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "ACBrightness", 10)
Else
EndIf
EndIf

I think it will be better to write it like this:

(this is pseudo code, I'm c++ programmer, just get my idea)

//in the beginning

runCustomization = RegRead( "HKLM", "Comm", "BootCount" ) eq 1

If (FileExists( "\Windows\RunCC.exe" ))
runCustomization = (RegRead( "HKLM", "Comm", "BootCount" ) eq 2)
Else
Endif

If (FileExists( "\Windows\Autorun.exe" ))
runCustomization = (RegRead( "HKLM", "Comm", "BootCount" ) eq 2)
Else
Endif

//later

If (runCustomization)
If (FileExists( "\Windows\Cook.mscr" ))
Run("\Windows\Cook.mscr")
Else
EndIf
BattSuspendTimeout = RegRead ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","BattSuspendTimeout")
ACSuspendTimeout = RegRead ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","ACSuspendTimeout")
BatteryTimeout = RegRead ("HKCU", "ControlPanel\Backlight", "BatteryTimeout")
ACTimeout = RegRead ("HKCU", "ControlPanel\Backlight", "ACTimeout")
Brightness = RegRead ("HKCU", "ControlPanel\Backlight", "Brightness")
ACBrightness = RegRead ("HKCU", "ControlPanel\Backlight", "ACBrightness")
RegWriteDword ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","BattSuspendTimeout",0)
RegWriteDword ("HKLM", "System\CurrentControlSet\Control\Power\Timeouts","ACSuspendTimeout",0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "BatteryTimeout", 0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "ACTimeout", 0)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "Brightness", 10)
RegWriteDword ("HKCU", "ControlPanel\Backlight", "ACBrightness", 10)
Else
EndIf

If (runCustomization)
//and so on...

The script will be easier to maintain.

The script will be two times smaller.