I still haven't purchased my X, but I've been working on cars for a while and have read this entire thread. It seems like the problem is electrical related, I'm willing to bet PCM.
Since SO MUCH of the engine is controlled by the PCM, and the 4R70W cannot function without the PCM, it might be worth SWAPPING IN A NEW ONE, or a GOOD used one from a working V8 2wd X.
I'm usually against "parts chucking," but in this case it seems like the common link between all the problems. Every problem that's been discribed can be traced back to control by the PCM. (Shift points, TC lockup, Idle speed, fuel injection, ignition) If the PCM was indeed going, vibrations, g-forces, varying voltage, moisture, temperature and other environmental conditions could have an effect.
I had a car that was running AWFUL, and a new MAS fixed the problem.... The MAS is the PCM's biggest and most important sensor for FI data. I'm not sure about the X/EEC V system, but on this car (BMW) the MAS contianed the environmental sensors such as Ambient air temp, barometric pressure...etc....
Another step besides just swapping in a veryfied OK PCM would be to somehow log all of the Inputs/Outputs of the current PCM and sensors. I know a product is made for the EEC IV to do exactly this, but I don't think one is made for the EEC V yet.
I have heard that Ford has a "Flight Data Recorder" that certain dealerships install. It piggybacks the PCM and reccords I/O, and after a problem happens, the driver hits a button and it records the past 30 seconds of data. On another chatboard, some people with Expeditions had problems where the truck would accelerate by itself, and they got these data recorders.
Just a thought.
-Aaron