Hi John,

I have a mustang too (95, but the plugs look the same), here is what I can see:
The top picture looks like it is the connector for the speakers (note the matching pairs of colours, one of each has a black line) from this I am guessing that all of the outputs from the amp are run back to these and fed back into the factory loom.
The second picture shows what looks like part of the Ford power connector harness, does this have a big plug on one end similar to the one in picture 1? also what is on the other end?
Picture 3, I assume the wires with the blue connectors on the end go to the Empeg sled? If so it most likely means the original connector has been removed from the sled.

From what I can make out from picture 2 it appears all of the wires that connect into the factory harness have tags attached telling you what they are for (I can see earth and lights easily), what you need to do is match those names to the names listed on page 6 of the user guide msaeger linked too, then connect that colour wire to the correctly tagged wire on the harness. Ideally you should check all of the wires in the harness with a meter first to check they are actually what they say they are, but I am guessing you don't have a meter to hand.