UPDATE - picked up the Expedition from the dealer on a Saturday morning. They found DTC P07E6 in the continuous memory. They replaced the maine valve control body (JL1Z-7A100-A) due to finding a "leak in the main control valve body halves". Their diagnostic states "found transmission neutralizing when trying to shift from 5-3, and going into neutral causing code P07E6".
Driving home about 20 miles all freeway, I noticed hard shifts from 10 to 9 if I went to accelerate. Then it got worse and worse, then finally it wouldn't go into 10th gear. Trans temp jumped to 246, and I noticed white smoke behind me (maybe coolant overflow steam?). When keeping it in lower gears (1-7) I noticed some hard shifting, but the worst is a delay in shifting between 3-5 (feels like it stays in neutral for 0.3 sec). Trans temp went back to normal and stayed normal while I babied it back to the dealership.
5 Days Later - Get a call from teh dealership saying it is ready for pickup. Using the FordPass app, I can see they test drove it a total of 5 miles. Per the tech's notes, the literally re-replaced the exact same main valve control body (JL1Z-7A100-A). This time they attempted to clean the main control valve but could not get the clutch latch valve to move in it's bore. They told me Ford said they likely got a defective main valve body the first time and to replace it again... Luckily, all of this is under warranty still.
Anyway, I pick it up after the 2nd maint valve control body replacement in 2 weeks, and it does in fact drive much better now. It shifts into 10th gear again, and 90% of the shifts are very smooth. I have noticed that the shift between 3-5 is still funky. It doesn't make a loud clunking sound liek some other thread discussions have noticed, but it still feels like it hangs in neutral for 0.3 seconds. I know it still has to go through it's "learning process" again, so I'm hoping that will smoothen out over time, but honestly I have very little faith. I also noticed when in sport mode (4A activated), it does make a very low clunk noise and has a hard shift into 2nd gear. This is worse the harder I accelerate. I had a 2015 F150, and it also shifted a little rough in sport mode, but I feel like the F150 was how it should feel. The expedition still feels like something is wrong to me. I will give it a week or 2, see if time helps, but I am convinced the weird "neutral for 0.3 sec" feeling isn't normal, and most other expeditions do not experience this unless there is an issue. I'm not sure what else they can do though, short of replacing the transmission.