A while a go I too had a clunk somewhere in my drive line of my 91 Toyota. I hunted around for loose components and never ended up finding it until I made the swap from my standard 4:10 differentials to 4.56. After I replaced the rear diff, the gears where still good but there was a lot of play in the carrier bearings holding the ring gear. The noise I had was an irregular "warbling" when going +120km/hr with neutral gas. If I let up or put gas down, the noise would go away. That source of the noise was hard to pin down. I also had drive line clunk/bang when I when I threw the truck into reverse in the mornings when first going to work. When it was getting bad I had to use a bit gas to "break" the rear into position, as the ring gear was so loose that it was binding up between the ring and pinion gear. That noise sounded like it was coming from the transmission but since it was fine going forward I started contemplating a transmission swap. Both noises when away after swapping differentials. At that time the truck had about ~450,000kms on it. If all else fails it might be the rear end.