A little hard to tell, is that a 5 pin or a 4 pin connector that was shorted? Do you know what it would connect to?
As for starters, check power rails and check resistance on the pins of the connector. If you can find a ground somewhere in the system, check voltages on each pin and reference that to what should be there (why knowing what plugs in is important). While powered down, you can also measure resistance between each of the pins in the connector, if you find something that's near a short, the damaged part(s) are probably connected to those pins.
If you find a power rail that is way under, you've probably damaged something in the power circuitry, so you want to see what is connected to it that could be the problem. I think it's unlikely that you just blew some protection part given where the connector is and that the rest of the unit reacted like that.