I too have experienced that on my 2001 SR5 4WD Sequoia. At 45,000 miles, when the transmission shifts into to overdrive, coasting (warm) from about 25 MPH to 35 MPH, it would skip or hesitate and then, clunk into gear with a loud thud. I recently took it into the dealer and reported the problem and a noticeable humming or a grinding metal friction noise coming from the transmission. When I would deactivate the overdrive button, the sound would cease. The mechanic could not hear that. Nothing was done. When I took it home from the dealer, that night, it clunked into overdrive gear again at a slow speed coast, 35 MPH. Three days later; today, my wife and my self are unable to move the column shift into park or 2nd or low gear. What's going on!!!. I'm taking it back to the dealer first thing tomorrow. I'll let you know what the outcome would be. I had to start in neutral to park and depress parking brake for safety.
I'm talking it into the dealer.
I have had similar problems with the transmission and lots of problems with premature brake wear. I now have a vibration when applying the brakes that shake the entire vehicle. I paid almost $400 to replace front brakes. This will probably be my last Toyota. My other car is a Toyota Avalon. Numerous problems with it since 1997. Toyota is no longer building a vehicle that lasts with no problems, like it did in the past.
This is a known problem by Toyota and it affects thousands of Sequoias. Toyota has openly admitted it on Toyota letterhead to at least one owner that I know of. My Toyota dealer admits to the problem, and also admits that Toyota has no intention of fixing it.
Vibration from floor boards on 2003 Sequoia is a front diff problem I had it replaced under warranty and it fixed the problem.