Thanks again...so I've rerouted wires back to their original locations and checked ohms on wires, still seems to be stumbling. I haven't driven it because I want to pull the plugs and check to see if one possibly fouled out during all the love the vehicle has been showing me
@greasemark...do you mean start the vehicle and then remove the batter cable? Positive I presume you mean??

 

maaaaaan...the "rough idle"/stumble seems to minute, that someone not looking for it might not even notice it. I feel it while sitting in the drivers seat. I can feel a slight hesitation and when I look at the engine it seems to have more off kilter movement as opposed to it's normal steady running.
With the rough idle being this small, not throwing codes and not triggering CEL...could that still cause trans to shift irregularly? "Could such a minute driveability issue cause the trans to shift irregular? I would think it could but it barely moves the tach...I know that's somewhat irrelevant.

 

Here is a pic of plugs...all wires were between 4k-6k ohms...

 

as I pulled all the plugs, they appeared to be good but cylinder 2 seemed to offset it's original gap of 0.48 to >0.25 and had some build up on the ground electrode. Is this normal from heat and could this be the culprit...

also the cylinder 2 spark plug doesn't seem to seat as far as the other plugs (same plug that regapped itself)..

 

you need to look inside the spark plug hole and see if there's any chance that the threads are damaged. If any plug doesn't seat the right way it will cause loss of compression and make the engine miss maybe just enough to go unnoticed to the pcm. some of plugs can be a real bear when trying to put them in strait.

 

I've tried, not possible even with dentist mirror. My finger can only feel a portion of the hole...
Is there another way to tell?

I also feel as if I can keep turning it, (it's very difficult) but doesn't stop like the other plugs.

 

It sounds like the plug was cross threaded when last installed. One of the things you can try is to ,buy, rent borrow what we call a thread chaser, when used carefully it can most times save a cross threaded hole. It would not be wise to attempt to do anything with the wrong tools or you could possibly end up having to remove the head to do it correctly with a thread repair kit if there isn't enough room to do it while the head is installed.
This is one of those situations where someone who has actually done it on that particular model vehicle in that particular cylinder maybe can further assist you.

 

One step ahead of you...kinda. Well I purchased a chaser and it did produce quite a bit of metal shards.
It's still not seating fully. I'm hoping this is the source of both my issues?!?!

 

That would be a very good bet. The other plugs looked just fine (but are they platinum? It does make a difference for the misfire monitor, but not right now). These plugs always were a bitch to replace, anyway.
As for as the trans goes, what exactly is it doing? Please be specific. I used to work on them, but Hanky is better at everything then me, so I might have to rely on him!

 

And it was the fat red wire that goes tothe alternator; just remove it and insulate it and drive to re-evaluate.