that breather above the exhaust man (where u have the little filter) is meant to be plumbed into your intake as this is meant to be metered air, this Fat hose runs over the rockercover and into your AAC Valve(Auxiliary Air Control) Which is part of your idle control...
As this pipe is sucking in unmetered air after the AFM it does not know what is going on and not allowing enough fuel to help it idle. So weld on a pipe and connect it up after the AFM...
As for the Rocker breather at the Back this is plumbed in B4 the Throttle body so any blow-by gets spat into your intake and burnt for Emissions Control as Jatsvl has stated above. Non PCV valve controlled.
Much like the front Breather Hose which is controlled by You PCV Valve (Positive Crankcase Ventilation) at the Intake plenum.
Thats why ur getting sh*t Idle man and a rough tune.
Like this man as long as the AAC valve is "Seeing" metered air.