Be advised, I'm doing this from memory, seek a second opinion.
Looking at your first picture, the orange and brown wires are from what looks to be your left coil, as you sit on the bike. Looking at your third picture, what you're thinking is the stop switch wires, are from the condensers, located in the mount bracket above the coils. The wires in your last picture come from the points plate, orange left, gray right. Referring to your second picture, the wiring coming from your harness, you have double plug orange and gray wires and single plug orange and gray wires and pair of red and white wires, plus a ground wire. Connect one condenser wire and the orange wire from the points plate into the double orange connector. Connect the brown wire from the left coil to the red/white wire. Connect the orange wire from the left coil to single orange harness wire. Do the same thing for the right coil, its just gray instead of orange, and you'll have to imagine the orange wire on the right coil is actually gray. The ground wire from the harness can be attached to one of the coil mounting bolts.
Hope this helps, I'm sure others will chime in with either confirmation, or other ideas.