I'd like to know how they blew the head gaskets on a 351W. They are pretty durable in that department.
The idle air control valve is cheap enough to replace. Search everywhere for vacuum leaks. And do not under estimate the ability of the EGR valve on these engines to cause idle and smoothness issues. A crack in the up-pipe from the manifold or a faulty valve can cause havoc. These engines DO NOT like unmetered air entering the plenum anywhere. Be it from the fresh air duct (past the mass airflow sensor), or anywhere the manifold might get air OR any gasses (ie: EGR).
Take the throttle body off and clean it with a throttle body cleaner solvent (not carb cleaner). Also the throttle position sensor on the bottom of the throttle body may be haywire. And dont forget the EGR valve back behind the upper intake coming from the pass valve cover.
The deal is...it could be many things and checking stuff (like the throttle position sensor) is an easy, but technical process. You need a factory manual really to troubleshoot. The good news is this problem is usually easy to fix, once discovered what it is.
As far as typical things you'd mod on a Mustang...like the intake...those things don't always translate to improvements on trucks. Especially heavy work trucks. The power/torque ranges are different for different applications. An Edelbrock intake could cause low end torque to suffer.
At least its not an OBDII engine starting in 1996. OBD 351W's are a little trickier to mod on little things like exhaust etc.