I would check fuel pressure and delivery volume. Almost sounds as if it is being underfed whenever you get some demand for higher speed. I make the assumption that you swapped one of the COP units to see if the misfire followed, and it didn't. Ditto with the spark plug and injector?
The fact that #1 is the one singled out for tattling by the system does not mean it is the only one. It may just be the strongest of cylinders, and its output is noticed more when missing by the system. I think the crankshaft position sensor CPS, is used to calculate the angular velocity [rotation speed] of the crank after each cylinder fires. When the rpm's drop a misfire is assumed by the ECM. At least that's how I would have done it. So a good cylinder not getting fuel could be called a misfire, but in actuality is not spark related..
tom