The smaller connector with 2 wires is only for re-programming of your ECU. Don't worry about it.
Ironically, your ECU may be partially fried... it's ironic because a code is thrown if the OBD-II interface goes out. And you obviously can't read said code.
You're already on the right track. The red or black wire on the main OBD-II connector may be your culprit. If you have a multimeter, just check them out.
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