[JSeery]

The filter should be before the pump to protect the pump. A filter is always a restrictor to flow to some extent, the finer the filter element the more it restricts flow. One solution is more filter surface area (larger filter). Not sure what type/size filter you are using, but on these applications I use the large canister or spin-on type. I would also add a regulator and a by-pass recirculation system if it doesn't currently have one. I know the Ford 5.0 injectors are sensitive to fuel pressure.

If it was my setup I would use a remote fuel pressure gauge mounting inside the car so I could monitor it during operation (electronic remote gauge). Mount a pressure regulator as near the throttle body as practical with a by-pass back to the tank. And install a spin-on fuel filter. The condition of the fuel tank and fuel can also be issues.