A friend put in an aftermarket cd player in my 2000 lincoln navigator and all my allumination lights quit working. What was done wrong, or what should be checked. Already checked all the fuses and the mechanic I just got it back from couldn't figure it out..

Either a Fuse blew that you can't find, a wire was disconnected, or maybe a wire was disconnected and connected to the wrong spot?
Live in South Florida?
If you have a Service Manual with a schematic, it will help with locating the particular fuse, and the color of wire involved.
Good Luck

Don't know the exact fix for your lincoln, I have much more experience with gm cars. But your problem is a result of an open circuit on the dash illumination caused by removing the factory headunit. Most aftermarket radios do not accept dash light dimmer commands from your headlignt switch like your factory radio did. I don't know the exact fix for you but the nice folks Crutchfield.com will difinatly be able to help you out. Sorry I couldn't be more helpful.

Here are some colors of wires involved:

2000 Lincoln Navigator Stereo Wiring Information (http://www.the12volt.com/installbay/stereodetail/1323.html)
The Blue/Black is your illumination wire, you may want to disconnect and try again, You could place a tone on that wire and follow through to a switch or a fuse?