The engine has 40k on it and runs like a top. U-joints are good. In 1st at 3000rpm the clicking sound is slow in 3rd at 3000rpm the sound is much faster. So i think that rules out the engine. The sound is from the center of the truck and not the rear diff.This is all in 2WD
My 84 22R stock 4Runner with 346K miles makes a clicking noise in every gear but 4th. I am guessing since 4th is 1 to 1 ratio thats why the noise stops. Under down shifiting the noise goes away also. I would like some suggestions. Complete rebuild of the "G" Trans or look for a "W" series Trans...