Nice conversion with the MSD, I think it's the best modification that every MOPAR should have. Anyway, I think your car after '71, so....
1. Yes, you still have to have the Voltage Regulator installed on the firewall because it works along with the alternator to keep the battery charging. If you remove it, the car will shut off when the battery drains. All today's alternators have a voltage regulator, but installed inside them. The two wires (green and blue) coming from the alternator are connected directly to the Voltage Regulator. I would leave the remaining wires as is, but of course connect the small red wire from MSD or if you also use the MSD Distributor, connect also the second red small wire, with the blue - tracer (blue/white) which goes to the bulkhead connector, so as to get current from ignition.
2. Yes you can, there is no reason to keep the ballast resistor when you have the MSD installed. Ballast resistor was installed back then to provide resistance to the flow of electricity in the circuit. No need to keep it in you car.
3. I believe it provides resistance to the flow of current to the electronic ignition box. No need to use it anymore. MSD has it all working!!!