Dellman,
If your truck is bone stock, you have a externally regulated alternator and the clicking you heard is the death scream of a bad regulator.
I have linked a good wiring diagram for a '66 which shows it as you have described.
Good luck and let us know how it develops.
http://rmcavoy.freeshell.org/diagrams/66engine_6.jpgEDIT. If you are not a purist, switching from the DN alternator (yours) to the SI alternator is simple and will get rid of the firewall mounted voltage regulator.
Stuart