Test your Stator/Rotor assembly - the (usually yellow) wires, when metered between two of the leads should show some level of AC Voltage (check your repair manual for details on how much and precisely how to at what RPM). There are so many aftermarket R/Rs - I've purchased and used EMGO (generic replacement) on my old EX500 - it ran fine. YMMV...
Just in case you want to understand what's happening on the inside - highly simplified:
This is more likely the case with your bike - a three phase AC stator/rotor combination, and a three phase bridge rectifier:
