For me, I took the stock values for Spark from the SVT program. That was the biggest thing.
TP for WOT was also an issue with the standard duratec ECU. If you are using an SVT TPS you should look at that in the tune if you can, or mention it to your tuner.
I'm sure there is more that I can think of, but if you have any more questions about this I will be happy to answer as I have done a lot of the trouble shooting in this area already.
