The harness in question is the "Engine Room Harness" and all models have F36 which is the important connector. I've gone over the wiring in as much detail as I can further down this post.
You appear to be missing the ECM relay - let's go over what's supposed to be in the relay box on a V9X engine. Note that there are six "spaces" on each side of the centre of the relay box, so I'm describing each space.
On the side with the fuses, from left to right:
- Fuse block No 2
- blank
- blank
- Transfer shut off relay-2
- Transfer shut off relay-1
- Back-up lamp relay
On the far side, left to right in that photo:
- ECM relay
- Front blower motor relay (the brown relay)
- Transfer shift low relay
- blank
- Transfer shift high relay
- blank
Okay, let's have a good look at the wiring diagrams. This is how it's supposed to be connected:
IPDM/ER fuse 59 (10A, 2nd from end near middle of side away from chamfer) to wire 14 in IPDM/ER connector - supplies ignition power directly to the gearbox via a YELLOW wire. This should be in a black 6-connector plug E18 but definitely ends up in F36 (staying as a yellow wire).
V9X-specific: Fuse 67 and 68 (both 10A) located in the fuse box with the transfer case fuses. Connected via plug E24, these fuses supply power to the transfer shutoff relays.
IPDM/ER fuse 25 - supplies continuous power (not switched by ignition) to AT through F36 - probably wire 2 (red).
E7 connector joins to F8 --> throttle control actuator.
E12 connector joins to F36 for ignition switched power on F36 pins 1 and 6.
F7 connector goes to body ground and connects to F36 terminals 5 and 10.
F36 connector goes to AT (round-sided green plug, 10 possible connectors)
Ground circuit: F7 body ground goes to F36 terminals 5 and 10.
F36 Connector has the following wire colours:
1 - "Sealed Outer" - Battery positive (ignition switched) (connects to F502 wire 9)
2 - Red - Battery positive (connects to F502 wire 10)
3 - Blue
4 - Gray
5 - Black - Battery negative
6 - Yellow - Battery positive, switched by ignition (connects to F502 wire 4)
7 - Light Green
8 - Pink
9 - Brown - Starter Relay Signal (from E17 wire 48) and to TCM connector F502 wire 8)
10 - Black - Battery negative
The manual does NOT specify the signal names for each of these wires (I'm annoyed at that). I've listed the items based on circuit diagrams elsewhere in the manual. The main circuit diagram for the transmission control module does NOT list these items, only that 5 and 10 are earth and the other wires are supposedly used.
The MANUAL transmission does NOT have any plugs like the AT does, but it does have a connection for the "backup lamp switch" and the "Park Neutral Position Switch". They are both 2-pin rounded connectors. The Backup Lamp is located lower on the rear right hand side of the gearbox, the neutral switch is above it.
The RE5 gearbox has SIMILAR plugs to the RE7 gearbox but from what I can see, they should all be functionally the same (F36 appears to be identical on both cars).
I really don't know how much help that's going to be. I've been through the service manual for several hours and can't make any more sense than the above.
However, at the very least, you now have the important wires and their colours for the plug that connects to the gearbox.
I truly hope that's been of some help!