I was able to move the boot underneath the coil pack for cylinder 2 to cylinders 4 and 6. 4 and 6 fired fine and 2 was still not firing, so I am ruling out a bad boot at the moment.

The only thing I can think of at this point is a faulty ECU since the wires were completely shorting out with the original wire harness, maybe some electronics were fried?

I'm not sure how to test the signal wire for the coil pack, only checked the voltage with key on engine off seeing 12V.