I was only in it for a few minutes. Long enough for me to unhook the strap from the front of the truck, hook it onto the back, hook it up to a D90 that was behind me, and he had to tug a few times to get me out. Couple minutes at most. The trans controller wasn't "dead", just wet. Soon as I cleaned it out, it worked fine. In the meantime, I drove around with it unplugged. I had P, R, N and 3rd gear. They have a limp home mode built into the hydraulic circuits.
That happened in August. I flushed it with 5 gallons of ATF. I drove the truck until the end of October, stored it for the winter, back out in April and it failed in May. There was little to no indication it was going. The shifts were a smidge slow, and sometimes the 1-2 felt a little funny. (normal people wouldn't pick up on it) The day it failed, it was almost instant. I was cruising in 4th on the way to a trail, it started whining, I tried 3rd gear and it was gone. I had to stop at a red light, and I could barely move. I got it about 1 mile up to the rendezvous point, and that was it. They had to tow me to Land Rover Salvage which was luckily only a few miles away. 2 days later, we went to pick it up. It was now cold, and I cleared the codes, and drove it right up onto the trailer. Flushed the trans again as it was cloudy with clutch material. I drove it a bit after that, but didn't feel confident in it. It felt funny, threw codes again, and I knew it was going to strand me again, so that was it, I parked it.
I'm not sure what could be done to prevent it, short of just never driving in water, which means never going off-road at all around here. You can expect to water ford on a class 2 utility road around here. If it came in the oil pump, then you have to stop it getting in the bellhousing. There's a drain hole cast in the bottom. And water can get in around the crank position sensor, the starter, the two rubber plugs in front, and the inspection hole on the bottom.
The JK guys local to me have been killing clutches in the water. It comes in the drain hole, and mud gets stuck in the clutch somehow. They don't change gears in the water. If they have to go in reverse, they shut off the engine, change without the clutch, then start it up in gear.
I'm planning on trying to seal it out as best as possible. I've already siliconed the slave cylinder. I might do the starter and I'm not sure about the CkPS yet. I'll seal up the drain hole, then drill and tap a new hole in the bottom for a good old fashioned wading plug.
My argument with Musky was never about whether or not water could break a truck. It was about the continuous suggestion that a D2 is just SOOO much worse than a D1 because of the electronics.