Update - Jan 2013
Car is back and it's going back together.
I rebuilt the main front harness with new, correct, crimp-on connectors and it's now installed and re-connected to the fusebox and all interior connections.
Cracked open the heater box to find the usual: decrepit foam turned into dust. Cleaned it all off (goof off is amazing stuff) and recovered the vanes and heater core with new foam.
Some black schmutz along the interlocking seams to better seal the box
Finished and with the foam at the firewall interface point in place.
Did a similar treatment to the evaporator box. New expansion valve and checked for integrity at 130 PSI. No bubbles. New layer of tar tape over the pick up coil for the valve.
Same story with the intermediate piece. New foam edges.
Base back in place and finally all in.