The act of rooting in itself can not make a phone slower, freeze, faster, or anything to this extent, this just isn't a factor when gaining root access
So it must be something you have done since you gained root, can't say what specifically but if its only been two days just think back to anything you did in this time.
I will say that many/most ram managing apps are more of a detriment than a performance to your phone, my first advice would be to stop using an app killer and just let android decide how/when to kill apps
And yes, over clocking is not always a good thing and can have negative effects, you seem to have figured this out already so if you have anything changed in regards to CPU change it back to stock settings
If you really can't figure out what is causing the issue then wipe clean and reinstall rom
Sent from my Nexus 4 using XDA Premium 4 mobile app