RX8DriftRacer

I'm having issues with my freshly built engine for some reason I'm getting a p0410,p0661,and a p0302 code I cleaned the connectors in back of my intake but I have headers on my car and the exhaust manifold doesn't have a tube like the stock one does its just a mounting point for the air pump can this be a cause? I'm also getting a rough idle from 1k to 750 rpm's which I hope is just from the break in process. can anybody help?