Yes you are correct.
Now back to the question at hand. I would suspect that you checked the wiring harness connectors and they checked out ok.
1.When you swapped the coils to a different location, did the misfire code change??
2.Do you have a scan tool that can monitor misfire data??
3.After you disconnected the battery and reset the module, which codes came back??
4.Did the U-XXXX codes come back??
Most U-codes are generated because of low battery voltage or module communication software error. If you cleared the U-codes and the didn't come back, don't worry about them. Since a U-code will not cause a misfire concern, lets focus on the misfire codes.
5.Inspect the crankshaft and camshaft position sensors?
6. Check the MAF sensor and the air intake hose between the intake and air cleaner for cracks/torn.
7. Can you watch fuel trims on your scan tool and record the readings during misfire??
Please let me know the answers to all 7 of my questions.