My 98.5 sounds like it's running good when I first start it but after it gets warmed up it idles rough and acts like it's missing or something. The guy that had it before me put a edge comp in without a lift pump so then after he had to put a rebilt injection pump in it he took the edge off and put a predator boost/ fuel box on it. It also tapped into the injection pump. I got it and unhooked that but it still runs rough when it gets warmed up. Maybe it has bad injectors? It's got 269,000 miles and that's when my dad replaced the injectors in his 99 cause he was losing power.

 

try simple stuff first...fuel filter etc......

 

Besides the simple stuff, try pushing a bunch of injector cleaner through it. Though with that mileage, it's probably past time.

 

any other symptoms at idle. exhaust smoke? color? what is strange is the fact you are saying it goes rough once warmed up.
do you have any gauges. do you know what your fuel pressure is at idle?
see any fuel leaking or leaks around injector lines.
and also you didn't mention it but get the codes pulled. rent a reader or go to a parts store that will pull them for you for free.
and like SIXSLUG said try the easy stuff check your fuel filter? who knows when it was last changed

 

I think its already been suggested but first thing is to remove all the added electronic hp stuff. Bring the truck to stock and see if it still does it. If it does then establish when it does it. Meaning does it only do it at idle or does it still if you ramp the throttle or cruising or..... It may be that the injectors are also not stock and they're simply out of calibration or if they are stock then they're just old.