Well I may have found the issue. I finally remembered to go out and have a look with it nice and dark outside, and sure enough, I got arcing going on with that number 4 wire. It looks like a bad connection down towards the plug, that's where most of the action was. It also shot some random arcs on the other side where that wire goes around the back of the motor. I also some a little arcing on the number 1 and 2 plugs.
Also, I revved it up while I was watching, and the arcing actually went away mostly, which explains a lot. Remember this wire tested out at less than 10k ohms resistance, which should be pretty good. Definitely didn't tell the whole story though. Whenever I get paid I will grab a set of Autolite wires and throw them on to see what happens.
Edit: Went and looked some more, is it normal at all to have arcing right at the end of the boot where the wire goes over the plug? I ask because cylinders 4,5, and 6 all had a bunch of arcing at the actual spark plug like that. The more I watched it the worse it got on #4, too. It was shooting all the way up the wire almost. Cylinder 2 had a pretty nasty one too.
