Did you check the accuracy of the tab on the timing cover? There are two timing tab/harmonic balancer relationships, one with TDC at about 12:00 and another with TDC at about the 2:00 position. A balancer/timing cover mismatch is not uncommon on engines that have been cobbled together from bits and pieces.
Jerry
Jerry, I hear ya. Best as I can tell you, the engine didn't come with one and I purchased and placed one in what should be the proper location on the timing chain cover. Additionally, when I set the mark right at zero on the timing tab, I stuck a short screwdriver in on the #1 spark plug hole, and could feel the top of the piston. Feels right to me.