I decided to do the same, disconnect the bypass wire at the ignition, run the bypass wire through the firewall and to the coil. I also upgraded the 6 cyl Mustang to a 3 ohm Flamethrower coil, per the Pertronix help line, they said that the coil would run cooler with that 3 ohm Flamethrower. So far, so good with the Mustang also, it does seem to run better with the bypass wire.
I painted up both new Flamethrower coils, to give them a sort of stock look, with the yellow top, and got the Autolite coil decal, which may not even be technically correct, as I think a late 65 or early 66 coil would have had a FoMoCo stamping, but since they dont have that decal yet, this one will do.
I also show a picture here where I ran my bypass wire, so future people can get an idea of how I tackled getting mine through the firewall, in my case, at the hose that goes through the firewall off the mainfold and connects to my vacuum actuated switch inside the car to open the rear vents. The Mustang was a similar situation, I had a non used firewall plug that I drilled through and snaked the wire through that into the car and then the bypassed resistor wire.
One more strange thing. I was going to, for just visual purposes, going to hook back up the now disconnected old coil positive lead to the coil positive terminal, instead of letting it dangle there. For shows and such, it just looks better that it is connected to something instead of sitting there unused. I thought by disconnecting the resistor wire inside the car off the ignition switch would ultimately render that wire now non voltage carrying.
To my surprise, when I hooked up a multimeter to it, on both cars, after all the work was done, I am still getting a 1 volt reading coming through that wire, even though it is no longer connected to the resistor wire that it would go to through the firewall.
Is that just residual voltage coming from some part of the system. Seems strange that something disconnected can still have one volt of current going through it. I choose to leave it disconnected in the engine bay instead of letting it sit on the positive coil terminal, but I dont understand why it has current going to it when it was clearly disconnected at the pink bypass wire inside the car.