I am going to guess that for some reason the engine is never moving to closed-loop operation. Drive it a while and get it nice and hot then take it to an auto parts store and have them scan it and look at all the sensor readouts and see if the engine is in closed-loop. If any of them look strange, then you may have a bad sensor.
The factory coil is going to be superior to any aftermarket coil. Get a factory coil from a wrecker and I'd bet the ilde miss goes away.