Figured I should update...
Dealer changed the front 3 plug well gaskets again. They said that Lincoln requires the gaskets to be changed twice before they escalate the problem to include additional parts/service. Fingers crossed it's sealed now.
They changed the 3 front plugs for free while they had it apart and, of course, gave the car a bath. Lincoln dealers really are pretty nice to deal with.
That allowed me to finish the steps above. 3, 4, 5, and 6 completed!
6 was interesting. After the reflash, the car was running horrible. Didn't want to idle and was sounding like a small diesel. Several emails back and forth with Torrie about the tune, map sensor, etc and all seemed to be fine on his end. The strange part was the the gas gauge was also reading that it had zero fuel. As in zero miles to empty.
I shut the car off and restarted it a few times and each time it showed I had more gas and the idle improved. By the fourth time restarting the car, the gas gauge read normal and the car started to idle fine.
I think I just have a finicky/slow learner car or something. All is good now and I'm comparing two different tunes.
Things are on track again with the S. Just hope the leak is gone so I don't have to undo the work for a dealer visit.