hey jong
about the engine miss, i'm not confident in my knowledge of these trucks yet to troubleshoot them for someone else. i'd hate to mess you up.
but the fass install i have done. i completely removed all the stock lift pump/filter parts and ran 3/8" line right to the VP from the FASS a couple years ago and have had no problems and never below 15psi.
if i remember correctly the instructions read to pump through the stock set up. i think it works fine either way but if you're going to add mods that require a lot of fuel flow, you'll be restricted by the small banjo fittings surrounding the stocker parts.
honestly i truly enjoyed removing and dumping the stocker LP. cleaned up the engine compartment imo.
good luck, jeff