Splice everything into one if you are going to use the original coil + wire(s). Sounds like the brown goes back to the "start" circuit. Make sure. Hook your meter to the brown and twist the key to "start." if it comes up battery voltage sounds like it is so There is at least one wire at the ballast you don't need I detailed that above. It went to the original OEM box.
Look at the diagram you posted. J4 going from ballst to OEM box is not used
J3-13BR(own) looks like the coil wire
F5-18B(lac)K is not used it was the OEM coil NEG
The two connections at the left side of the ballast in the diagram are essentially jumpered together, as "one"
So jumper those two to the coil brown and hook the old coil brown as power wire to the new Pertronix
