when certified ford dealers get rebuilt engines they get them directly from fomoco so they are built properly, what most other people are talking about are engines that you get from like pep boys,auto zone, and all those other chain stores these motors are not rebuilt by ford but through a private contractor which means they are junk if ford is replacing the engine you should have no problems with the engine and will be able to do what a new one can have done to it.
not to mention your ford warranty and they do all the work