Buy a set of cheap copper plugs and throw those in and see if the mis fires go away, that will set you back $12 and 30 min of work.
If that cures it then your good to go, if not then dig deeper.

Keep
It
Simple
Stupid

 

Update: before trying a plug or wire swap, out of necessity I started driving the truck short distances for a few days- according to other posts at a risk of fouling my cats or O2 sensors (hopefully I haven't done that!)
However, after maybe day 4 of driving maybe 5 miles a day with some start/ stops, a miracle occurred- spontaneous smooth idle!!!!!! As I think about it, maybe not completely spontaneous but close. The first 1 1/2 days my CEL light would blink upon start, going to steady a few miles later, all the while running somewhat rough. Then, around day two, the light remained steady, and idle seemed to improve but was still a bit rough. Then, at day 4, I went to start the truck and PRESTO- no CEL light and an idle smoothness that is close to great, but still not perfect.
I have to summize that the light and the trucks performance are connected. Was the computer brain purposely changing the truck's mechanics while on, only to reverse the change once cycled through?
This seems odd since my mechanic tried resetting the light many times after his absolutely correct install of the plugs and wires, only to have that light come right back on.
One would think if you get the work done right, the CEL responds accordingly right away. What gives? And should I trust that all is well now?

 

At the top of your post you mentioned a ceramic donut on the coil side of the plug wire. Your new wire did not have it. That was fine in the end? It sure looks like you would be loosing contact with out the larger diameter connections. I am doing the same wire swap today and it feels funny.

Thanks

 

how did the wire swap go bbolin? Mine still seems to run fine. Apparently Magnecor does not use the ceramic "donuts" so both ends look the same- in fact aren't both ends the same, or interchangeable?

 

Unfortunately I am still getting a miss out of #6. I am getting P306 error code. New plugs and now new wires it may be time for coils. That should be fun!
It just seemed odd that the ends of the wires were that different then stock. I guess if they work all is good.

 

Was this issue been resolved? I'm having the same issue,sparkPlugs(new champion double platinum), plugwire and coil was replaced less than a year.

 

The donut is a guide for the plug. My STI wires didn't have them either and made it harder to line up and plug into the coil pack.