Have you checked the camshaft timing? With the valve cover removed, turn the engine in the normal running direction (clockwise from the front) until the #6 exhaust valve begins to close. Just as the exhaust closes, and the intake begins to open, the #1 and #6 pistons should reach the top of their stroke, #1 on compression, and #6 on exhaust. One turn of the crankshaft later, the #1 cylinder valves will "rock" and #6 will be at TDC on the compression stroke. You can monitor piston position with a bright light shined into the spark plug hole, or by probing into the plug hole with a piece of soft wire. Don't insert a stiff tool such as a screwdriver into the hole, as a mistake while turning the crank could result in cylinder head or piston damage.
It's beginning to sound like the cam has been timed a tooth late on the timing gear. The engine will run that way, but it won't run right!
Jerry
