SECONDARY AIR INJECTION CODES AFTER ENGINE SWAP

I did not unplug the harness on the air pump under the bumper, just put it aside after I removed the two tubes from engine. Connected them back. Is it possible it is due to the fact that the intercooler is not yet connected so the air isn't like or where it should be or the amount is different? Don't worry about the cam code that was because I forgot it unplugged/ So I have 2 secondary air codes, the ambient temp cause it is unplugged, cooling fan cause it is unplugged still, and the one that am not sure why it is there the intake manifold runner control stuck closed, don't know what it means or where to look