When the deck lid should be closing do you have power on the orange wire at the deck close limit switch. Even though it gets jumpered to the yellow/violet by the switch there should be no voltage on the orange wire.
Does the convertible top manual you have have the schematics for the 12 relay system. Most of the ones I've seen do not unless you have a later version. Use the 12 relay schematics in the Technical Resource Library instead. I will look at it and see if I can give you some suggestions. I've had a couple '60's with the 12 relay system and the harness is closer to what Concours sent you with the bullet connectors. Is there a part number on the harness anywhere. I'm wondering if someone replaced it with a different harness.