I really appreciate the advice. I'll look more into the wiring when I get home. I'm going to solve this I won't give up. I'll report back with my findings

 

I decided about six months ago that I would do my best to prolong the life of my brothers 2002 Sport XLS hoping to add maybe 50k + if possible.
My first stop was fix OIL LEAKS... (requires removing the intake)... anytime you take something off, good practice is to refurbish/clean etc.

Short version:
1) removed intake replacing valve covers and gaskets/tube seals, spark plugs, plug wires, rear cam seals, cleaned intake plenum/throttle body etc.
2) some 2+ months later, reassembled and it was running terrible. Super rough idle with tendency to stall.
Nursing the throttle to higher RPMs smoothed things out but with an occasional misfire.
3) First thought was I missed a vacuum line or who knows but couldn't find any.
4) Since the ignition coils are right on top I removed the connectors from the IGN Module and the only one that made a difference was 3/6. The other two virtually nothing.

Somewhere along the line someone must have been troubleshooting and swapped the connectors/wires for ign coil 5/2 and 1/4 (Stamped on intake).
I'm assuming during my assembly I matched the Power Transistor connectors (from a pic I took) but used the stamped numbers to orient the plug wires.
This left me with the PTransistor trying to fire 4 cylinders at the WRONG TIME. Only 3/6 were timed properly.
The thing ran bad but apparently 2 cylinders is all it requires.
Swapping the 2 coil plugs made her happy again.

The behavior sorta sounds similar. Just something to check off the list.

 

Thank you. There is a chance maybe I swapped the connectors and didn't realize. They seem to naturally flow to each coil but I'll try it.

 

Thankfully I solved the issue. I was chasing misfires but it wasn't due to spark. Turns out the injectors were clogged with trash. The 4 that were misfiring cylinders 1346 we're almost completely clogged. I cleaned them out and the truck run like a new one again. This thing has been a headache but I'm glad it's over. Thanks again for the help everyone

 

Hi, I solved this problem very simply. I cleaned the spark plug and lit it. Now I'm thinking about changing the oil, which oil is better Motul vs Mobil 1. I advise you to read an interesting article. If you change, change the oil, because it is not as difficult as it seems.