Is the polarity correct from the mag pickup in the distributor to the MSD box?

You verified this by swapping the two wires and saw that the way you have it has the timing retarded compared to when the wires are the other way?

Or you just know the colors are what they're supposed to be?

I've seen both the distributors and control boxes have the polarity of those wires be incorrect.

i just verified the MSD by colors. this box was in another car running normally. The distributor is another story. I have other one to try out once the motor is back together.