I found the lights in the INL section of the FSM but the schematic doesn't give a clear indication of how it's physically wired without digging through pinouts and such. I think you broke the circuit to the lights that are out when you did your rewiring but can't eliminate a loose connector.
Reconnect the wires that you didn't use. Connect the ground wires to ground and the illum power wires to an illum power point.
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