Here's a quick update on the progress to date. Both local dealers told me there was a 3 week wait, and that I'd have to drop my truck with them and leave it the entire time. One eventually told me that since mine is a fairly new truck, just over a year old, and with low miles, that they'd try to push me to the front of the line.
Ultimately they got my truck back to me on day 6. Given the circumstances, I was cool with that.
Navigation system - They fixed it with an update. I can now search for, and find, addresses. If your navigation system suddenly lost the ability to find addresses, this may be your fix.
Moaning Brakes - they said they couldn't reproduce it so they did nothing. It moaned like a sasquatch in heat the morning after they gave it back to me.
Leak in the cab - they replaced the third brake light and told me it was fixed. It began leaking again as soon as I got it back, perhaps worse than when it went in. I had to give them the truck back and then wait. They've had it for maybe three days now, and they called to tell me the problem is the rear window, and that the entire thing needs to be replaced. Now I'm waiting for them to submit pics, get approval, and then see what comes next. They gave no indication as to how long the repair may take, or if the parts are available. I'll just wait to hear. She made it sound like the approval process should go smoothly since it's still so new.
Hood filling with water - I don't know if they fixed the issue or just drained the hood. It didn't rain hard between when they gave it back to me, and when I had to give it back to them, so I'm not sure if the hood issue is fixed or not. Their service department rarely answers the phone, and even more infrequently returns calls when you leave your number, so I'll have to ask them in person whenever I go to pick up the truck.