Retested AFM and everything is good except the air temp sensor.

I finally had to time to work on the car again. I put a refurbished air flow meter in it. The car ran like ****, FI 5 and 6 are not working now, but the continuity test was good at the ECU. The continuity for the air temperature sensor is still no good, just like with the old AFM...what would cause this?? The only thing that seems logical to me is something is wrong with the connector or the wire leading to it, which is bound in with a bunch of other wires or am I missing something? Any insight what it could be or where to start looking?