I've got a '81 Honda CB750 and what I know about this comes from this bike, so my advice might be slightly off from what is actually going on with your bike, but anyways here it goes...
So from the alternator, if it is a electromagnet and not using permanent magnets, then there will be a wire sending 12 V DC to the electromagnet, a ground wire, and one or more wires sending AC voltage from the alternator. In measuring the AV voltage coming off my alternator, I set my multimeter to AC voltage and it would display about 13-17 volts AC, or something around there, depending on engine speed. You can measure this at the battery too by setting your multimeter to the DC voltage reading and seeing how the voltage varies with engine speed. It should be around 13-14 for about 5000 rpm. So if your getting readings like that then you should be pretty groovy.
To test the stator only, select the resistivity reading on your multimeter. On my stator there are three wires. You want to test to make sure that there is continuity between all the wire on the stator. You can test to see if there is a short by connecting one lead of the multimeter to one of the wires and the other lead of the multimeter to the stator case ( any clean metal surface on the stator should do). If you get continuity there, then you have a short and the stator is bad.
Then you can test the rotor alone. This is done by measuring the resistance between the two copper rings on the face of the rotor. You'll have to look up what your spec is for that. Mine is about 5 ohms.
Also make sure that two brushes on the alternator case make contact with the copper rings of the rotor, and that they are not worn down past their scribe lines.
When I got my bike, I had this phantom electrical problem where my bike wouldn't go more than 10 miles without dying. Turned out that I had a bad connection at the regulator/rectifier, THEN the epoxy holding the wire core in place on the rotor disintegrated and broke a connection on the rotor, THEN my replacement rotor lost its spec resistance after one use! I ended up fixing the connection on my previous rotor and I've been relatively free of electrical issues since.
Good luck!