Well, based on excellent advice here, I did both coil packs, plugs and plug wires on my 4.6 Windsor when I did my timing chain tensioners (also new water pump while there). All parts installed were motorcraft.
Ran so much better, yet has set check engine light a couple times now (with clearing code twice now) after a few weeks. I've also checked gas cap of course. Fresh gas, new air filter, MAF cleaned thoroughly. Idles fine, doesn't miss going down road, no ill manners, yet codes for miss on cyl 4 & 7. Is there any trouble shooting that can eliminate or verify if it's oxygen sensors? I'm just guessing at this point, but would like to verify before proceeding. Because oxygen sensors are original w/180K I "tend" to "guess" perhaps it's them. But don't want to just start throwing parts at the problem. no miss, runs fine, yet throws code showing 2 cylinders misfiring.

 

also meant to type, no rotten egg smell, no exhaust leaks I can tell. And, I also have installed brand new fuel pump assy in tank by removing the bed, and I did new fuel filter at that time. And, my idle is stable and same as always, no searching or up and down, rock solid.

 

O2 sensor can not cause a miss code.

Pull off the spark plug wires and blow out the spark plug wells with compressed air. The most common causes for misfires on fresh spark plugs are: water or debris down in the spark plug well, cracked or torn COP boot or spark plug wire end, faulty COP, broken COP electrical connector or injector connector, & damaged spark plug. Remember, new parts can be bad right out of the box including spark plugs and plug wires.

 

I agree with Sam, probably electrical............. I did chase a miss fire on a 4.6 motor a few years ago.. In the end, it was a bad fuel injector....... just a thought, when all else fails.......... I put in a complete set.

 

Oh well, cleared codes, drove it today. Not a miss anywhere, I guess the check engine light will reset in about a month. That seems to be the pattern. There is no corresponding miss to the codes when they do set, it's like a glitch. At no time in the last couple months since both new coil packs, plugs, wires has it missed even once, yet it'll set an "emissions related code" according to my Actron scanner for 2 cylinders misfire, of which I do not see or hear or feel, and gas mileage still same around 16 mpg.

 

How odd is this, Ive got to replace my fuel pump, and Ive had both these exact 2 codes come up just before i pulled it into the garage to drop the tank!

 

I'd already replaced my in tank fuel pump months prior to this starting. By the way, been driving it since my post, it hasn't reset codes. I really thought those codes said like emissions related, so I presumed I needed to change my stock 180K oxygen sensors.

 

possibly humidity / water on a couple electrical connections that eventually evaporated or burned off.

 

interestingly enough, since my initial post, my check engine light came on again, and I didn't bother to clear it. Couple weeks later, last night, it went off all on it's on. Truck has never missed at all during any of this.