Greetings, I have a frankentruck with some weird problems. (The engine and frame are from a 1998 and the rest is from a 2001. I rebuilt it two years ago after crashing into a tree. Truck has 154k on it now.)

As of recently my truck has had a really rough idle (sometimes stalling) and trouble starting hot or cold. The engine is a 1998 2.5L.
In the past year or so I have replaced:
-cylinder head because it had sunken exhaust valves
-fuel filter
-timing belt
-water pump
-idler pulley
-fuel pump (twice replaced, the second time it fixed the P0171 code, hesitation, and a misfire)
-IAC (smoke tested, found it was leaking internally)
-MAF (swapped multiple times)
-EGR valve
-coolant temp sensor (to PCM)
-DPFE (was replaced with a plastic aftermarket sensor, but the replacement was faulty so the original is back in and seemed to have fixed that problem)
-coil packs
-spark plugs and wires
-a variety of hoses that were leaking (smoke tested)
-O2 sensors
-fuel injectors
and probably a few more. The truck has been well maintained but I'm out of ideas as to why its running so shitty.

The truck used to have a dead misfire after I got gas, no CEL. Rough idle has been a problem since before I replaced head.
It was my grandfathers truck so I'm trying to take care of it and keep it running through college but I have had this car apart too many times and its always giving me problems. Any advice/help is appreciated! :)

Also: since I have both a 1998 and 2001 computer I have swapped between the two.. the truck runs worse with the 98 PCM and smoother with the 01. With the 98 computer and the code reader hooked up, there is no O2 voltage or vehicle speed read.

 

Unplug EGR valves vacuum line while engine is idling, it should have no vacuum on that hose at idle, so idle shouldn't change a bit when you do this.
If idle changes then EGR vacuum switch(modulator) is bad, it is leaking vacuum and opening EGR valve a bit, when you remove the hose it is now a vacuum leak so idle would go up a bit.

If no change in idle use another vacuum hose on the EGR valve and suck on it, see if idle gets even worse or stays bad, if idle doesn't get worse fairly fast then EGR valve is stuck open a bit which is fouling the idle and starting.

And just as an FYI:
The dual spark plug/dual coil system on these only use the Exhaust side coil/plugs for starting, intake side coil will not work until RPMs are above 500.
So don't think "hey it can't be a coil/plug problem I got two, so no start can't be that".