Good Luck Josh and Keep us posted!!
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I also noticed on the car fax that the vehicle was serviced at 39k miles at an independent local mechanic and they flushed the differential and transfer case fluid. Is it possible they used the wrong fluid or amount of fluid and this is causing the problem?
The differential and transfer case don't share fluid with the auto transmission so I can't see how it could be linked, as long as your transfer case and differentials are working as they should and are quiet I wouldn't worry.
It's only when you make an abrupt stop and then get on the gas again that the problem appears.
That is exactly what happens when the fluid is low and sloshes around when braking and getting on the gas from a stop. It's during the sloshing the shifting problem occurs. Perhaps they just didn't add enough fluid the last time they were flushing it.
Update: I just picked it up from the Toyota dealer this morning. They installed a remanufactured transmission and replaced the water pump and timing belt since it hadn't been done yet (12 years old). Everything seems good. However, I noticed that the ECTS power and 2nd start switch is not working, nor is the light illuminating on the dash. Also, the light won't turn on if I press the traction control button. I checked the fuses in the engine compartment and a few in the kick panels.
Any ideas? Is it possible they didn't connect the ECTS switch on the center console when they took it apart to replace the transmission? Or, a fuse that I overlooked?
For the amount you probably just shelled out at the dealer, I would be asking them these questions...