Mike, yes, you can use the stomp starter with the new harness, etc. If your ignition switch has off/acc/run/start positions, you'll be OK. You really just need off/run. You simply won't use the solenoid wires.
In the run position, you will have a circuit connected from the battery to the ballast resistor to the coil. This will allow your engine to start and run using the stomp starter. This makes the assumption that you are using a stock points ignition system. If you use an HEI, you can bypass the ballast resistor because you don't need the voltage to the coil/points to be reduced from 12 to 6 volts.
You should have a small terminal on the side of the stomp starter switch. Run a wire from this side terminal to the + side of the coil. This allows 12 volts to go to the coil during starting when you stomp on the starter switch, but the contacts inside the side terminal disconnect when you take your foot off the stomp starter. The ballast resistor takes over once your foot is off the stomp pedal and allows the coil to operate on 6 volts to keep from burning out the points. The extra voltage from the side terminal of the stomp starter is to create a hotter spark to help with starting.
An alternator is no problem. Wiring will depend on if it is a one wire or a three wire alternator. If you are running a one wire, you simply run a wire from the battery to the alternator. You're done. If you are running a three wire, you run one wire from the battery to the alternator, another to your main junction lug to allow for remote voltage sensing for the voltage regulator, and the third is what is called an exciter wire. It tickles the alternator to function when the ignition is switched on. (One wire alternators are self-exciting, but they will only produce power once they achieve a certain RPM while a three wire produces power once it is tickled when the ignition key is switched on.) The exciter wire needs to be run to a switched ignition wire. The feed side of the ballast resistor is a good connection point. You will need to wire a diode into the connection at the alternator or else the engine will not turn off when you turn the key to off. You can buy one at Radio Shack and solder it into the harness yourself or you can buy a pigtail that has one wired into it that plugs into the alternator for about $10 on ebay. You can sometimes skip the diode if you run an idiot light off the exciter wire because the idiot light will create enough resistance to allow the engine to turn off when the key is turned off, but the diode is a bullet proof way to make sure, idiot light or not.
Sounds complicated, but very easy once you sketch it out.
Matt
