Im looking at a manual and an auto harness side by side. The auto harness has the black and yellow wire going from c-15 out to the transmission. It does not return into the cabin. I have two open wires now. Black with white stripe and black with yellow stripe.

The black and yellow in the manual car never passes through the fire wall. It instead gets run to the open pin on c-08.

If I just run this wire to the empty pin on c-o8 will it work properly is the ignition wired differently?

I can't find the starter plug on the manual harness. And I think the colors are different. What are the cookies for the starter plug wires?
First image is at second is mt

I've swapped a few auto mitsu cars over to manual. There is usually one large plug that plugs into the transmission. Two of the wires in that plug will be a lot larger than the others. I cut them, tie them together and solder them and this bypasses the safety switch and allows the starter to turn over when you hit the key. I never bother with any of the plugs under the dash. Is this what you're asking?

That was my original thought on the matter. Then I noticed the differences while adding a shield to my knock sensor. I figured I'd post my findings. Thanks for the response.