I've added a seperate electric pump back by the tank and a seperate spin on fuel filter as well. I did leave the old FFM in place too because of the water in fuel sensor and the fuel heater.
Quite a few guys have done the same thing in one way or another.
We run an fs1000 fuel water separator with half in fuel line from tank to pump and mount pump and filter down on the frame rails. Done this to every diesel i've ever owned. Completely taking the stock stuff off....