Quoted from pdman:Woz, a lot of times the wire colors in the System 1 harnesses don't match up with what the manual says.
Some games (like my Genie) don't have the correct colors listed initially, but do have a correct code for each wire. Like they changed colors mid-way thru a run. More info at the link below.
http://www.pinrepair.com/sys1/index.htm#flippers
(scroll down to Gottlieb wire colors)
This obviously doesn't account for colors fading, which makes things tough. When in doubt, check the colors of the wires on either side of the wire in question.
