On the mustang, the NsS wires that are in the harness with the reverse lights are merely jumped together. So you would splice them together.
On the 5-spd, there is a clutch safety switch, and then on the top of the trans, a sensor that tells the computer if the trans is in neutral for code dumping purposes.
Is this an EFI swap?if so, there will be a few other harness you need to pay attention to to domit correctly,