Servicing the transmission fluid is always a good idea and apparently needed doing anyway, but what you describe doesn't sound the the typical AT shudder that people with 5AT FJs usually have. Did you check the drive shaft universal joints for play? Even a tiny bit can make a lot of noise and vibration sometimes.I have a shudder and it's drivetrain. All week I have started to notice a faint but growing growl. Then yesterday the shuttering started to become unmistakable shake when accelerating and decelerating. As I coast to a stop I can click my automatic transmission over to neutral and shuttering stops completely. Staying at a steady speed is just as smooth as can be.