The next step will be to check function of #6 injector- make sure it is pulsing and has good spray pattern. Also, pull #6 plug and inspect for gas fouling, this would indicate a injector leak.
Also, you need to do engine cylinder compression test. Low compression can indicate possible valves not closing completely due to carbon deposits which would cause misfire
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If you do a compression test and that cylinder is low, most auto repair shops have a fuel induction cleaner that goes straight thru the intake vacuum that is great for cleaning carbon deposits.
You may even want to try that anyway to clean the injectors and see if that corrects it.
Re-reading the part about intermittent CEL light coming on, I am leaning more towards an injector issue. First, pull the #6 plug and check for gas fouling, which would indicate either leaking injector or one that is just shooting a stream. To test spray pattern, pull injector and have some one crank engine while you hold paper to injector at an angle. Proper spray pattern will be about 70degree fan pattern. If its narrow fan or stream- injector is clogged.
If no evidence of a leak- swap injectors and see if the misfire travels to the cylinder you swapped injectors with. If it travels then you know to replace injector. If it doesnt, then next step will be to get a noid light(available for $10 at parts stores) insert the noid light into #6 injector connection and crank vehicle. The light should blink steady, if it doesnt then it is not getting injector pulse from PCM. At that point you will need to start tracing for an open/short in harness from #6 injector to PCM.
IF all the above check out- then do the compression test.
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yes, just come back to this question and re-open it. Let me know what happens and if you need more help on troubleshooting it. The first Accept is all you need for this problem. I will stay with you until its running smoothly