No the reference is to the new junction. I had to separate the old junction wires because the alternator is now on the passenger side of the engine. I replaced my alternator output wire with an 8 gauge wire wire so I didn't need the old output wire for that, but I used it to power my coolant fan. My battery charge wire and the cab feed wire were long enough to reuse. One wire I forgot to mention is the black/white 18 gauge wire for the ammeter. It was soldered into the old factory junction so I just connected it to the new terminal with the alternator and battery charge and the ca feed wires.
The other ammeter wire that connects on the right fender junction runs straight to the cab firewall block and then straight to the cluster plug to termina 12. I ran it to to the terminal strip to a separate terminal and continued it from there to the cluster plug.
It is much easier to separate the old soldered, or crimped junction, wires and just do away with it. I am sure the wires aren't going to reach the junction so I would unwrap the harness and just use the one's you can and replace the rest after you reroute all of them then you can retape all the wires for a clean look.
Just remember that all the wires you connect to your junction will be full time hot, and any keyed on hot wires like ignition and start and accessories will require a different junction or switch.
It doesn't matter which wires you connect to the junction, they will all be connected together.I would connect the alternator output, cab feed and alternator sensing wire, to one big lug, and the battery charge wire, and fan power wires to the other big lug.Then you have the smaller terminals to use for other relays.The brown exciter wire for the alternator to no. 1 on the alternator has to be keyed on power so, it will need to run to a separate connection or else straight to the alternator if it is long enough.