I've got an 05 FX4 aswell. I upgraded my 6 CD to a Shaker 500 unit out of a mustang and I too, installed the factory sub out of a Lariat truck.
The plug for the sub at the H/U was taped to one of the support brackets on the left hand side when your looking in. There was a protective plug taped to the end of the harness to protect the ends.
As for the plug at the amplifier end, mine was located by the rear seat (SuperCrew) at the slit by the leg. All I had to do, was reach in and grab the wire and pull it out, plug it in and Voila...... Awesome Sound, especially with the Shaker 500.
I've heard that all the 04's were pre-wired with all the plug-in's and on the 05 models, some got the all the harnessess and some only got half. You can goto Ford and get the plug-in for the amplifier end and and just run new line from the back upto the front and attach it to the existing plug that's there. The power comes from the deck.....
Hope this helps,
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