If the issue were a vacuum leak due to a bad intake gasket, I'd expect that at a minimum you'd also be getting codes for lean bank 1 and/or 2. Since you are only getting codes for coil primary/secondary issues, I'd be more suspect of the Camshaft Position Sensor (CMP) or wiring issues. Some of the Duratechs had harness issues that I thought caused fuel injector issues, but you may want to look in to the wiring harness issues to see if that also impact the coils.
-Rod