I know this is a tad old but thoughts bring me to a couple questions.
How does one prevent the frame rail pump from struggling to bring fuel thru a aftermarket fuel filter or fuel/water separator setup?
Seems as the OEM upper filter could be swapped out to a H&S kit, but then you may loose micron rated filtering capability. So if you added a lower micron filter on the lower pre-pump supply side that should help, but could cause flow issues thru to the lower pump.
I have to think one wants to prevent water more than trash (within reason) from getting to the lower pump. Install a good aftermarket water separator using a 25micron filter, then use the OEM filters in stock locations. Wouldn't that be the "best of both worlds"?