Ford truck running rough, no SES light

I have a 2002 F-150 Supercrew with a 4.6L Triton, and she has 94350 miles. The truck ran fine until about 2 weeks ago. While down the freeway, it started running rough. Felt like I was going down a bad gravel road, then suddenly the SES light came on. It would burn steady, then flash for a few minutes, then back to steady. I took it to my mechanic who put it on the computer and got a reading that the number 6 coil pak did not even exist. He replaced the coil pak and after a few more tests he ordered a new computer module. When the computer came in, he drove the truck to the Ford dealership to get the computer programmed. The truck ran perfectly without a single miss. He did not put the new computer in. He put the truck back on the diagnostic computer again, no errors. He even pulled hoses, etc, trying to get an error and never did get one. He told me that he had absolutely no idea what was wrong with the truck. I got in to drive it home, and a few miles down the road, it started the missing again. No SES, but it still is running rough. And the truck doesn’t run any better at 75 than when it does at 25. Doesn’t make any difference with speed nor if OD is off or on. I can’t take it back to him because he is retiring at the end of this month. I know very little about vehicles so I posted this on a Ford truck forum. Here are some of the replies that I have gotten:

May have a problem with your wiring harness and/or plug at the PCM.

This peticular fault does not set a code because it is intemittant and load sensitive. Have the tech stress test all the coils looking for one with low output.

Ford doesn’t use misfire counts to set DTCs the way other manufacturers do. Why? You have to ask them. Misfires are one of the few CONTINUOUS Monitors for most manufacturers whereas other systems in the vehicle only get tested once in a while(NON CONTINUOUS Monitors). Misfires are important because they can cause so many problems and can be caused by a lot of different things.

Did the mechanic leave in the new #6 coil? Maybe that reduced the severity of the problem enough to keep the SES off.

"He even pulled hoses, etc, trying to get an error and never did get one."
So maybe it’s time to try the new PCM.

Yes, he left in the new coil. It may have reduced it enough to keep the light off, but it’s still running the same!!! hahaha. Thanks.