Thanks for the recommendations.
After reading through the Ford repair manual and the Haynes manual, I've decided to remove the head with the engine still in the car.
I had a shop look into restoring the threads (helicoil) with the cylinder head on the vehicle, but they were concerned about dealing with the 12-inch "access tunnel" to where the threads are located (they were hesitant to use extensions on their threading tools) and the restriction of being located right next to the firewall.
I'll pull the cylinder head this weekend and have new threads installed (helicoil or locking steel inserts) by a machine shop next week. As long as I've got everything apart, I'll install MSDS headers in place of the restrictive OEM manifolds (with those failure-prone precats). Both of my Duratec MTX Contours will then have MSDS headers.

Pulling the cylinder head to perform the repair will also give me the piece of mind that there are no metal shavings inside the combustion chamber.