Coils will have no effect on the PCM. If you want to anyway, disconnect for 30 minutes to be sure, but like I said, it would be pointless.
Look for something else. Shorted or broken wire (read resistance through them, they should be an even progression for 1, 3, and 5, then a bit more for 2, 4, 6). Also try cleaning the coils with rubbing alcohol. There may be a high resistance to ground if the coils have solvent/dirt etc. on them.
Read the resistance of the primaries and secondaries, and compare them to your old ones, or re-install the old coils and see if the symptoms improve.