In previous testing with MAFS, Pro-M, modified stock ones, etc, I have found that when we used modified stock MAF's we would get this condition, bad idle, hard starting. First thing I would suggest is to put the MAF screen back in. Since you have the Mirko adapter, the screen will fit. I am thinking that the Pro-M may be leaning out the motor and causing a CEL for a lean condition. If your idle continues to be rough, with the MAF screen installed, it is more likely, as already mentioned, a calibration issue with the MAF. Swap back to the stock MAF and see what happens, to eliminate this possibility.
AS far as the IAT, as long as it is connected, that shouldn't give a CEL but ensure that the sensor end is at least protruding into the pipe. I made sure of this before the BAT pipe was installed on my SVT.
