you should be able to tell by the length of the wires and the original crimp/grouping. The first two wires near the main connector go on 3 and 5 (on the back).
The next "group" of wires goes on 4 and 6. The longer one of those two goes on #6 since that is farther from the middle. The two lone wires go on 1 and 2 if I remember correctly off the top of my head.The longer one should go on #2 since it is farther away.
I had this same problem when I was figuring out my manifold but I had another 3.0 car and extra harnesses to try to copy. for some reason the wires were not identical between my harnesses though so it was confusing.