I don't know when Merc changed colors but on the later models (3 cyl 90) the CDI modules each have a yellow/black stripe (or black/yellow stripe if you don't see it...one goes to kill the CDI the other goes to the fuel enhancement/choke solenoid)....forget which and my manual is gone.
In the control box, this wire is grounded (connected to battery -) when the key is in the OFF position and as such grounds the triggers to the CDI modules, thus killing the ignition and stopping the engine. Since you changed harnesses, problem is likely to be there. It could be a corroded pin in a connector, or a broken wire,