The heads should. I'd pass on the intake though. Trucks need torque.
I literally have an 03 f150 with a 98 mustang gt manifold. I have torque from 2-4000 rpm now instead of 2-3200 however I would honestly for your mustang look at the Ford racing performance intake manifold or see how much more power you can get with cams before you upgrade the manifold. I changed my manifold because my trucks aluminum one warped and needed more power overall especially in the higher rpm's where this engine makes power without being stroked out. And you are using non pi 4.6 bottom with pi heads so your compression will actually increase anyway giving you more power than a stand alone pi 4.6. don't quote me but I think you might be getting 10:1 if not 9.8:1 . If you are using the manifold on a truck then get ready to do some runs to Lowes to make an intake and throttle cable bracket.What intake should i get pls , i look at American muscle and idk which one 2 buy