Yes, my dizzy is in backwards because I rotated the engine and placed it with the valve cover on figuring I had a 50/50 chance of getting it right. Of course Murphy's law prevailed so I just rearranged the wires.
I don't think you can put the flywheel on out of sync though due to the pins. They are not equal distances. i think the flywheel only goes on one way. If you had a flywheel form a different motoer (like in my case) the marks might be irrelevant.