Hey the66mustang,
The "ballast resistor" is the resistor in the red (+) line between the ignition switch and the coil. It is unded the dash. It takes the form of either a small (usually white) box or a resistor wire that is marked as such. This resistor is placed there by Ford to reduce the coil power to 6 volts. When using the PII this resistor can be eliminated as the PII is designed to run with a 12 volt coil. The Flamethrower II is also designed for this application. If your coil was supplied with a resistor of its own I would not eliminate it. In this regard, however, if you are using used parts you cannot be sure the set up was not modified by a former user who may, or may not, have known what they were doing. Bottom line, don't use used parts unless you have done the research and know exactly what you are looking for. Many of us have found some very odd mixes of parts on what should have been stock cars. These things are many years old.
Enjoy - Steve