OK. I spent quite a bit of time and could not get it. Looks like the white/purple colour appears when you don't get the right colour.
I think I will just use 'Light Manager' App as that does what I want.
So much is happening that lots of questions are getting lost!
Rebas - did you manage to get green? I can get light blue then orange, it seems to skip green? I set 'Green' in WhatsApp but have not had a message to check. I am not sure if CM Notification program overides an Apps colour choice?
I added a new Application in CM Notification program for TXT and EMAIL, and at least email works, not had a txt yet to check.
Remember 'Light Manager - LED settings' on Play Store is free and works well.
I have tried email, whatsapp and txt. It is showing the colours I selected and will show multiply notifications one after each other.
I could not get it (updated System.apk) to work using ES Explorer. But then again I'm a noob, so just edited the ROM using WinRAR with new System.apk on PC and reinstalled ROM.
If you use GoBackUp, Tillaz (Infusion ROM creater) recommends this. Then a ROM reinstall is not much of a ball ache. You can be up and running quite soon.
Apps + settings, TXT & Call Log all backup up nice and simple.
I would not install another Kernel at the moment. I thought there Daz has done things to help/improve JB so changing the Kernel might cause problems.
You can OverClock the standard Kernel anyhow so why do you want to change? - Goto: Settings - About Phone and keep taping ' CyangenMod Version' or 'Build Number' and you will become a 'Developer' you then have a 'Performance' menu in Settings that you can O/C etc.