I recently had an interesting failure on my 1998 4Runner. The symptoms were reduced power, ~20% lower gas mileage, and an occasional miss/hesitation. The miss was taken care of with new ignition wires and plugs and replacement of one coil. However, the reduced power/higher gas consumption remained. It was eventually traced to a faulty timing belt pulley on the crankshaft. A piece the width of the keyway had broken out adjacent to the keyway and allowed the pulley to rotate back and forth about 10 degrees on the crankshaft rather than staying in a fixed position. This caused the timing to vary with application/reduction of power, causing the problem. When the mechanic ordered the new pulley (from Toyota), he was told that the problem was not uncommon and that they kept the pulley and bolt in stock because of that!
Just thought you might be interested in this failure.
Jim