First of all the crank turns 2 times for every one turn of the cam so the marks will line up every 2 revolutions of the crank. I think thats what you getting confused with the 6 and 12 o clock positions. Set the crank gear at the zero mark in the instructions.
well im short on cash right now i still have the engine in this time and i already replaced the head gaskets once im going to try the pain of glass thing with my push rods and hopefully they aren't then it will just be getting new gaskets for the front timing cover and intake manifold thanks guys i think thats all it was and that i didnt have my rockers torqued right