Well I finally had time to replace the plugs and check everything, but even tightening a loose throttle body clamp along with new plugs (tuning shop said plugs might be glazed) did not fix the issue.
Again, it is not a change in RPM, but a subtle idle pattern difference.
It used to be a nice steady "whuw whuw whuw whuw whuw whuw", and now it is "whuh whuw whaw whuw whuw wha, whuw whuw whaw whuw wha, whuw whuw whaw whuw wha".
I did replace the battery a few weeks before the MAF sensor debacle, Duralast Gold, and I also think the temporary after market MAF sensor might have changed idle or timing codes, even though the dealer reset them all. Both the old cleaned MAF and the new Ford MAF the pattern is the same, so I don't think it's the MAF anymore. The problem started when oil contanimated the MAF when I changed air filters and the truck died in sloped driveway.
I suppose since I am ordering a new Raptor, the dealer says there is nothing wrong, and only a true motor head will notice, I will just have to give up, but it bugs me.
Anymore ideas?