So I havea 2006 mustang that used to run like a top I put a set of msd coils ford blaster coils on it and car went downhill I put factory ones back on and still keep doing same thing from there I took plugs out and plugs only had few hundred miles on them but looked wiped out I put e3 spark plugs in it now when ever I disconnect the battery and reconnect it the car runs rediculous but as I drive it it seems car starts to go in and out of power like it programmed itself to run like crap sound like anything someone might know Al packer ford didn't c anything wrong with it I wonder if it the plugs or something electrical

 

You might have stretched the springs out in the original coil packs. I know our s197s don't like after market COPs. Have you tried new OEM motorcraft COPs? That's what I had to go with eventually, after purchasing some SLR performance COPs that my 05 rejected.

 

Check the actual harness connections where they plug into the cops If the little plastic tab gets broken, the connector will snap into place but may intermittently come loose. I chased this issue for a while once and it took me bit to figure it out.