Ignition wires get warm

Pertronix ignition draws current with the key on / engine not running.

"How long" are you leaving the key on? It is NOT GOOD for the ignition or coil to leave the key on for long, and it was never designed to do so. It is also possible that you might burn a spot on the alternator brushes / slip rings as the alternator will be drawing field current

WHERE is this wire getting hot?

Only near the switch connector?

Near the bulkhead connector?

Uniformly along it's length?

If near one of the connectors, this would most probably indicate a bad connector

If uniform along the wire, this indicates severely overloaded current flow, and you need to find out WHY.

Try disconnecting first one alternator field wire and recheck

Then disconnect the Pertronix and try again.

You have any other harness modifications, any accessories, stereo, alarm system, etc that's been spliced into the harness?