Bzizzi, Did you get 4runner fixed? Mine is doing the same thing and now when it goes into OD there is a thud into that gear. Not to mention the thud the trans does when at a stop and let foot of brake.
Bought my 2011 SR5 a few months ago w/ about 8k miles on it. at about 13k i am now noticing the transmission shudder and the driveshaft clunk...looks like i need to set-up a dealer visit....blah! the dealer i bought my 4runner from is an hour away, i hope the local dealer that i will address the issue with doesn't hold that against me.