I'm afraid I don't know much about Lincoln audio systems, however if it's anything like Ford's stereo systems you can buy a set of U-shaped tools at Auto zone or Advance auto parts that will allow you to remove the system from the dash and you may be able to remove the stuck CD with the system out of the dash (just ask for a pair of Ford radio removal tools). That's what I think your issue is over (just a stuck CD in the player/changer). Maybe it would be possible to remove the CD by gently prying it out with a toothpick that is if you can reach it. As for your driver’s side door the speaker or tweeter may have a loose connection or just gone bad. Regardless just take your time with it and you will get it working again.
Hope this helps,
Crossnine