I have a 2005 Tacoma with exactly the same problem. I started hereing the cherping or clicking before the vibrations started. You hit it right on the head! I could not have explained it any better. With that said, I can not figure out what is causing the problem. I read someone had a simmilar issue, but it turned out to be the drive shaft, it was out of balance. I am taking my vehicle to the dealer on Monday.
Harker Heights, TX