Ok, i think i got your problem from those pictures you posted. This is how it looks to me: If you unplug the harness, and are looking at it with the clip on top, so the wires are away from you, and the side you plug into the VSS is towards you, were going to say 1 is left, 2 is center, and 3 is right. this is hard to explain on here so bare with me.
So it looks from the picture that a yellow/white wire is in 1, a white/black or yellow/black is in 2, and the green/white is in 3.
Again correct me if i'm wrong, but if thats right, then you'll need to connect the yellow/white to yellow/white.
the white/black or yellow/black on the VSS to the yellow/blue on the vehicle harness.
Finally the green/white to the black wire on you vehicle harness. I'm not sure what car that VSS is out of, but its no factory honda. But it looks like that will solve the issue, because its deffinatly wired up wrong