I see you've been at it all day today. Sorry, I just got home a little while ago. Sounds like you've made some progress on your own though.
If you have the rear harness and the front harness disconnected, then I believe the only things left are the dome and courtesy lights and the wiring from the fuse box to the headlight switch. That big black wire concerns me. Not sure it's the problem but it obviously isn't stock. You said it goes to something behind a metal plate. The pic is too small to really make out what's what. I would unplug that black wire and see what happens then. You can email the pics to me at w70442@hotmail.com if you'd like.
Can't help with how many pins are supposed to be on the plug for the head light switch. Just don't know.
I haven't looked at the schematic but I'm almost positive that the things that should come on when you pull the head light switch straight out one click or one position is the two orange parking lights in the bumper up front, the two orange marker lights in the front fenders, the two red marker lights in the quarter panels, the rear tail lamps which have three bulbs in each lens(L and R) and the two license plate lamps. One on each side of the license plate.
You said that your dome light is working now since you replaced the harness but, and you probably already know this, the dome light and the two courtesy lights under the dash should turn on when you turn the head light knob all the way to the left(counter clockwise) regardless of whether you have the headlight switch pulled out one click or two clicks or not at all. Just turn the knob to the left all the way and the dome and courtesy lights should come on. You've replaced the headlight switch and it does the same thing so it's 99% ruled out. It's unlikely but possible that the switches are bad in the same way. So, assuming that the switch is ok, if the knob is NOT turned to the left all the way when you pull it out, the dome and courtesy lights are NOT in the circuit so they can probably be eliminated. IF, however, the switch knob was turned all the way to the left, then there could be a problem in that circuit. You said that the dome lights work though so I assume that means works as it should with out blowing the fuse.
That leaves us back at that black wire and the fuse box. As I said, the pic is small but I think I also see some other orange wires that appear to be just stuck into fuses. I would remove or umplug any wire that does NOT look like it was installed at the factory.
You're getting closer.......