Mustang missing after trying to start without transponder key

Okay so I have a '96 mustang GT and the other day the only transponder key I have broke. So I found a way to bypass it and use a regular non transponder ignition cylinder. While I was testing it, the car would start for a few seconds and then die out (part of the anti theft PATS system) So now it's bypassed and I can start it fine with a regular key/ignition but now the car has a mild miss. Could this be from the failed attempts at starting the car without the transponder key? Maybe it kept flooding it out as part of the anti theft. I haven't removed any plugs yet but it's acting like they are fouled out. I hope that's all it is. Any other ideas if that's not the problem?

There is a black ring around where you insert the ignition cylinder with a wire going to it from the transponder box under the column. It acts as the antenna for the transmitter. I removed the transponder from the broken key and taped it up with several layers of electrical tape perpendicular to the black ring. It's the best location I could find for it to transmit. Reinstalled my top plastic piece and the non transponder ignition. It works like a charm and even though it seems jimmy rigged, it's better to be able to have keys made for $1.50 each instead of $175. Unless you were a mustang buff and could make the connection of my car being a '96 with a regular key, no one would ever know the difference.

Soooo I found out why my car was missing



Threw in some new NGK's and it's running like a top. Thanks for the suggestions guys.