so, since the fuel relay repair, and replacing the fuel filter, I checked the plugs to find that one was cracked. I replaced 6 plugs on one side and I'm calling it a night. I went for a drive and the car is running much better. 4th gear in high rmps, the car misses, and feels like it's shutting down half the engine.
I've not tried to drive the car any distance to see if it's going to cut off after 40 miles until I can get this misfire completely gone.

The fuel filter poured black fluid out of the in line. I wonder if I got some really bad gas or something.