Spook,
It is not my intent to 'rain on your parade'
I am making these comments with a sincere hope of helping you out...
The CEL turning off doesn't mean that the problem has gone away.
The Diagnostic Codes should be pulled. Anything other than emissions equipment codes should be fixed.
For example... if you are getting a code for an O2 being rich/lean, and then you hook up the PMS and start tuning...
You will be chasing your tail and wasting your time.
You need to make sure EVERYTHING is in perfect working order before you start tuning.
Again, I'm not trying to be a dick, or imply that your Mustang is a pile of junk.
But the issues that exist now, will need to be fixed if you want to get some good tuning done...
jason