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Next thing is get a running compression test at hot idle. What you are looking for is a comparison between the problem cylinder and good ones.
I would also try swaping the fuel injector to another cylinder and see if the problem follows the injector.
One thing I always do is replace the fuel pump and PCM power relays before looking at the PCM. If the power supply gets "fuzzy" unexplainable things can happen.
Make sure there is no corrosion at the pcm connector and visually inspect the connector for backed out pins.
Yes, each coil has its own wire to and driver in the PCM.
I would be interested in knowing the short and long term fuel trim numbers at cruise and idle in drive.
An osillisope would be the only tool that would be usefull to compare waveforms of different injectors and the ignition primary. A different scan tool is not going to tell you anything more than you already know. It sounds to me like you know what your doing.
If I had this truck I would change the PCM and fuel pump relays and put another set of plugs. If that did not get me anywhere I would change the PCM.
I would rather spend my money on parts then diagnosis.