New here so please bare with me. I have a 91 f150 4.9 inline 6 with a lot of noise coming from what sounds like under the valve cover. So I pulled the cover and all of the push rods are not in the center of the holes in the head. Any ideas?

 

Check if there is side to side play in the rockers, also the rods might actually not be in the center, and see if the rockers are loose, or if they are adjustable check the lash.

 

Rockers are not loose. And it seems that only the push rods on the exhaust valves are not centered, they are rubbing against the side of the port in the head.