Navigation and RSES
I believe that the rear seat entertainment system did not change during the 3 year run ('03-'05). The '05 version will accept MP3s (supposedly), but I'm not sure about the '03 or '04 versions. Quite honestly, you're better off without it and buying a portable DVD (or 2) for less money than what the option cost. It doesn't take away any headroom in the 2nd row, but it does make the space feel more cramped. The biggest plus I've seen is that you can use the aux input jacks to plug in an iPod or other MP3 player to play music through the sound system.
I've heard the the navigation system was changed during the run. There were some glitches with the early versions which were subsequently fixed in later versions. I believe that the system is the same as the one used in the Navigator. I've been pretty happy with the navigation system in my Aviator. In general, it's been spot on for directions. If you buy an Aviator from a Lincoln dealer, they will send you DVD updates to the system every 2 years. If you buy one from a 3rd party, you may still be able to register it for updates. Ford did a nice job of integrating the nav system with the sound system, yet keeping the climate controls separate. Lexus integrates the climate controls with the nav system and separates the audio, which I think is more of a hassle.
As far as wiring harnesses, you may be out of luck. Though the OEMs generally try to commonize harnesses, in this case, because of the complexity, there were likely different harnesses for the following combinations: 1) base - no RSES, no Nav, 2) RSES only, 3) Nav only, 4) RSES and Nav. I suspect it would be a very tricky matter to add either option retroactively. Again, you may be better off buying a stand alone Nav system as opposed to integrating it into the vehicle. At least you could transfer it to other cars.