I have driven my 4Runner for 8 years, accumulating 120,000 miles, needing nothing other than planned maintenance. It's been a great vehicle. At the 120,000 mile routine maintenance, they noticed that water had gotten into my CV boots, and I had them both replaced. At this maintenance I also got the 4x4 fluid changed (which I am guessing included differential fluid...?).
That was a little over 5 weeks ago, and since then I have driven about 1500 miles, maybe less. I have used the 4x4 for maybe a total of 25 miles, only using it on snowy/icy paved roads for short periods of time.
So it was about 5 weeks between the CV swap, and the first point I noticed any unusual vibration. The vibration was irradic, and accompanied by varied levels of noise. Both the vibration and noise came and went over a two day period before I took it in for service.
Since this original post, I have called back the dealership and have gotten a little more detail. They feel that I caught this very early, and that I could potentially have driven the car for another 5,000 miles before experiencing a major failure. His best guess was that something broke in the front differential, causing metal shavings to be in the gears of the front differential, and that they were being washed out of the gears as fluid passed over, hence explaining the "coming and going" of the noise/vibration. He said it wasn't worth the time or effort to actually tear apart the differential to investigate, because it needed replaced nonetheless.
He did say based on the rarity of this type of failure, that he has their most experienced mechanic on it, the one they go to when crazy things happen. It is their belief that there's no way the CV replacement had anything to do with the front differential having shavings in it, and he did explain why, but I couldn't 100% follow everything he was explaining, because of my lack of in depth knowledge of this mechanical system (I am fairly mechanically inclined, but I don't know cars that well, and this is my first experience with a front differential).
I still find it extremely unlikely that the two events aren't related, and the Toyota guy even said it was the first thing he asked the mechanic too, because it seemed logical. However, I suppose if I were representing the service department, I would tend to think that we weren't at fault either. But, I didn't get the "you are trying to rip me off" vibe from the Toyota representative, who has appeared to be very sincere throughout this whole process. And my past experiences at this service department have been positive. I want to give them the benefit of the doubt, but at the same time $2000 is a lot of money, and if this was an avoidable failure I don't think I should be on the hook for the bill.
On a side note, I only drive this 4Runner on regular paved roads, and I rarely even use the 4 wheel drive. I don't drive off road, and don't push the vehicle very hard. It just seems off that something like this would happen to my vehicle, when these things are built to handle abuse.