When the Cycle-Electric alternator dies, or gets flaky, the engine will not charge any more and there will be a steady drain until the electronics packs up and everything quits. Before that there will be a series of 'strange things' happening.
With the engine running check the voltage using the stalk. If it's over 14 volts then that is not the issue. If it's under then replace the alternator/rectifier with the H-D unit. All my biker friends consider the stock rectifier a p.o.s., or to be kind, delicate...