Take pictures of what you are doing and help us out a bit!
My guesses are that you are using the alternator in the DC setting, alternators provide AC current which doesn't read well on a DC voltmeter.
If you start the bike, with the negative of the meter on a clean section of the frame, now disconnect the wires one by one, (I have an SR which has different colours), don't disconnect the black one. One of them will cut the engine out, plug that one back in, and test the remaining wire. It should be a brown wire you are testing, white/red goes into the CDI, leave it plugged in and start the bike. When you rev it you should be getting some reasonably high voltage, around 20/30 volts, perhaps more.
http://www.users.on.net/~madmitch/KDX/K ... iagram.jpg