All gaskets are new. Upper plenum, lower intake, head, and exhaust.
There has been plenty of kicking, screaming, and cussing.
The damn thing runs great off an idle though. Getting very frustrated.

Swap your #4 injector with your #3 injector and see if the misfire follows it over.

i wonder if the cat/ exh. is got a bunch of coolant in it backing stuff up, that will cause a misfire same as if the cat was bad.

If the misfire stays, swap your coil packs around and test again.

During my first troubleshooting, I bought a new coil pack, and injector. The problem was still there.
Do you think that Bars leaks crap is possibly clogging my cat?
No apparent restrictions off an idle though.

How would I check the cat?

You would have to pretty much dump that stuff directly into the cat to clog it up. So, I don't think its related.

Can you inspect your EGR tube for cracks? I've heard this can cause misfires also.

I just had it off yesterday and did not see anything wrong. I cleaned it out with cab cleaner also. I am getting a slight leak on the exit flex tubing where it mounts to the egr bracket though. I cleaned the mounting surfaces real good, but still leaks a bit.

Like I said earlier about the bars leaks, when I dumped it in and ran the car, it disappeared real quick, and the car exhaust sounded plumb full of coolant. Heard gurgling from the exhaust. Wouldn't the dealer have picked up on that though by catching a convertor code?

Get that leak fixed.

It is possible to check for a clogged cat using an exhaust back pressure tester. I see them listed EVEN at Walmart for $39. It plugs into the O2 sensor ports upstream and downstream.