I replaced both exhaust manifolds on my 4.6 3 valve 2006 Explorer. Quotes were about 800 per side I believe. Mine was ticking like nuts when cold, it bothered me every morning for 20 seconds, even more when driving next to a wall or divider on the highway.
I got both of them for about $ 100 each, but it took me a whole day for each side, and that included drilling and tapping 2 out of 8 each time. It's a b*** of a job, F150 is wider, but not much. Explorer is so tight there, you want to cry. I unbolted the motor from the mounts and jacked it up, and that helped. Now, it's still quiet but I know it will come back one day.
On filters, I was told that Motorcraft filter has some type of back flow preventer design, so when you shut it down, the oil does not drain completely from the top. Aftermarket filters do not have that. It helps with every start up if the oil is still sitting around timing components.