I have the exact same problem as the others - 2005 V6 4Runner w/ 176,000 miles on it. Feels like running over rumble strips when going about 30-45 and have foot lightly on gas pedal. Other than that the truck is running perfectly - engine is powerful and smooth, shifts perfectly, rides beautifully.
First I changed the transfer cased fluid thinking the problem was in there, but that didn't solve anything. After reading a lot of other suggestions I decided to simply change the transmission fluid in my transmission. Toyota says there is no need to service these transmissions, but they are definitely WRONG. There's a drain plug in the bottom pan and there is a fill plug on the passenger side towards the back of the transmission. This alone tells me Toyota had originally planned on making these serviceable. When I drained the fluid it was clearly spent; it came out like black thin fluid. The new stuff I put in (Toyota brand ATF-WS type
https://www.amazon.com/gp/product/B00CTUSEMU/ref=oh_aui_detailpage_o00_s00?ie=UTF8&psc=1 ) was red and a little thicker. It certainly needed to be changed.
On the first ride out I could tell it was so much better. No rumble and still shifting smoothly - definitely the solution to this problem. I was going to change the screen inside, but I didn't have a new gasket so I didn't chance taking the pan down and tearing that. But I will definitely purchase a new screen and gasket, and take the transmission pan down. This way I can check the magnets in the bottom of the pan as well.
It was a quick job to just change the transmission fluid - maybe an hour. Putting the truck up level on jack stands takes longer than actually changing the fluid. I recommend this for anyone having the same symptoms as described above.