Do you feel the vibrations in your feet (trans/engine/brakes) or in your ass/love handles (rear end/ drive shaft vibrations)? If you think it may be drive-line related, I would check to see how much slip yolk play there is or your drive shaft just may be unbalanced.
I noticed at the lower RPM's, my old slip yolk would cause a vibration but at higher speeds/RPMs the torsional force would "hold it" in place.
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98 4runner, 5speed, 2.7L 3rz, 370,000 miles, 2x4, OEM Elocker, 4.30 gears, ToyTec Ajustable Coilovers wit 500lb spring and lots of other goodies.