The coil and ignition wires have not been replaced. I guess next on the list would be the wires. They look fine and test between 1.1K and 1.4K. I wouldn't know how to test the coil. Is it possible that the wires do need to be replaced?

Yes, I have the egr unplugged and so far it hasn't gone into really bad running mode, it does still run noticeably worse when It gets warm. Unplugging the O2 sensor to force it out of closed loop has no effect either. The serious hesitation seems very random, and just when I think I've fixed it it will happen again.