"The Metra 5514, which includes the bypass harnes (Metra 70-5513) did NOT fit my 99 Contour. One end fits, but the car's other plug leaving the amp is a small square plug - not rectangular."
Maybe I'm not understanding what you're trying to do, but if you bought the bypass harness, I would assume you're trying to bypass the factory amp and power the speakers directly from your Sony deck. Is this correct?
If so, you don't need to connect anything to that small square plug. That connection supplies the low level output from the factory deck to the amplifier. The scary part is, it also supplies power to the amplifier; notice how small those wires are? The larger rectangular connector is for your speaker connections.
