I run the Pertronix in my TR6. The 3 is bone stock except for air cleaners.
In the 6, I tied the wires together at one point after exiting the distributor. I didn't take any particular precautions.
I would be certain to use a coil with quick slide connectors to keep the wires clear of the contacts.
My problem occurred when the insulated negative wire made contact with the positive post of the coil. A good quality wire would have protected the unit from a short.
I don't believe there is a problem with cross arcing through two sets of insulated wire, including the plug wires.