On each side harness (those that contain the front light wires, horn wires) there is a multiground where all the ground wires go to. There are thin and thick versions of the ground wires. When I return the harness to the car, as long as I match up wires to the correct gauge(ignoring where the wires originally connected to, and colors) I should be alright, correct??

 

Yeah, you're fine. Just so long as all those are grounded somewhere.