Quote:
Can I assume that the wires line up correctly?

No, I do not believe the Civics use standard ISO wiring layout.

Keep in mind the FAQ also says this in red:

Whatever you do, do not guess at the wiring of your car. You could blow fuses (or worse, fry your car's electronics) by trying to hook up 12 volt power to the wrong wire. You should always use the wiring harness adapter from the installation kit.
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Tony Fabris