Do you have any more info on this? I have a 2001 eclipse as well, and an empeg mk.2.

seeing that you posted this a month ago, you may have gotten past this, but anyway:
Here is some info on those harnesses:
from left to right on the back of the head unit:
small 8-pin connector with 4 wires: control of display pod as you know
13-pin cd-changer input. this must be a standard port on the back of these mass produced cd players, because it is non functional.
14-pin connector with 5 wires: orange/black is constant power, white/black is ignition sense, black/yellow is ground, green/white is illumination, pink is (i think) power antenna control.
6-pin amp control and outputs
the last two are antenna: right is for power antenna, both are used it you have one of those antennas wired into the frame (or so i've heard).

as for the amp pinouts, here you go:
http://www.neweclipseforums.org/ubb/Forum3/HTML/000190.html
this message board is very useful, if you haven't seen it. that post i linked to has some good info, and its a good place to address any specific 2000+ eclipse technical questions.