Janine - I worked for Western Auto/Parts America/Advance Auto for 4 years.
I have seen all the products in depth.
I think the Autolite Professional wires are good quality. Just probably not up the the factory stock wires IMO. (or Magnecore or FMS for certain) The coil pack ends are different so that's something right off the bat showing they are not the same wire set.
I looked at the Motorcraft vs the Autolites at over a year ago and they were different. The aftermarket Motorcrafts were identical to the ones on my car. So it does sound like they are not the same wires anymore. That stinks!
I know for a fact Stant does not make the stock thermostats for the Duratec. That is why I said it is very likely they buy them from Ford (Motorcraft) and re-sell them. Several other companies do not even make or offer t-stats for the Duratec. Robert Shaw is one of the only companies I found that actually makes one. (180 degree brass unit according to their catalog)