Ok, the large plug on the left in your pic is obviously the main power, speakers, ground, etc. The small one on the far right is to the subwoofer (brown positive signal - black negative signal , green = mute signal). Are the RCA outlets on the Nakimichi labeled positive or negative ? Or what model Nakimichi is it? Some use RCA jacks, some want you to splice into the harness. You'll find that the RCA jacks pair up with a couple of those other wires in that side of the harness, you just choose which ones you're gonna use. If you don't use the RCA jacks don't leave them naked to touch something metal or short out. Don't forget to put a 12v to 5v reducer in the AMP ON signal wire or you will get a nagging pop from the amp every time you turn the radio on. Ford amps only like a 5v ON signal, not the industry standard 12v that comes from aftermarket stereo head units.
The one in the middle is the parking aid mute signal (dark blue), subwoofer ON (light green / black), vehicle speed VSS signal (grey/black), and inputs from the optional rear overhead DVD player if you had it ( Red, Black, White, Light Green ). Since you don't have it, the only leads you might be interested in using are the parking aid mute signal wire (dark blue) and the VSS vehicle speed signal if needed ( grey / black ), and the subwoofer ON signal (light green / black ). If you eventually hook up a backup camera you can get the reverse signal from the harness over in the driver's kick panel.
-Mike
