I'm not sure why your ammeter is affected. You don't need to mess with shunts...current is current. The ammeter likely has a shunt built into it anyway because most meter movements handle only very small currents.
A ballast resistor is used in a points-type distributor, in-line with the voltage to it. A voltage dropping resistor may be used to lower the voltage to devices, usually to handle a change like a 6V to 12V conversion. I suppose technically you could call the ballast resistor a voltage dropping resistor but that is not how they are commonly referred to.
Wiring. Your generator has an output terminal and the alternator has one too. The output is usually the thickest wire. You probably have a generator warning light wire, that can simply be connected to the "1" terminal of your internally regulated alternator. This also provides the voltage necessary for the regulator/alternator to function properly. With the three-wire alternator, the "2" terminal needs to be connected to a 12V bus, i.e. where most if not of your electrical system draws from. It is this point that you want the alternator to regulate the voltage.
Do some research on earlier threads/topics. There is a wealth of information on this subject. You will also benefit by having a detailed wiring diagram for your vehicle to refer to. A good shop manual will have this information.
