Most after-market 5.0 -351W heads have holes drilled to match 95-earlier mustang. GT40P heads, and torquemonster headers are unique, the headers made for aftermarket heads will NOT FIT!!
I had to ship my set of headers back to Bob, he had to weld on the aftermarket flange so they would fit My Edelbrock heads. Been there.
So, if you have that set of headers, or one like it, they will not fit factory heads.
Edit--
You can "make them fit" but they may have a lot of port protrusion, meaning the flange will be blocking off some of the port.