With your meter set to Ohms, test from each stator wire to the bike's chassis then battery negative.
Stator wires should show as connected together, but never to chassis or ground. That would be a reason why it might not be charging.
Test is stator output, after charging your battery back up with a low current, gentle battery charger like a Battery Tender, disconnect stator and start the engine (bike up on center stand) set your meter to 200 Volts AC and measure stator output at idle, then rev the engine, AC voltage should rise with engine speed.
Your Rectifier converts AC to DC, then your Voltage Regulator drops voltage down to about 14 volts.
Shut the engine off, reconnect stator, start the engine (bike up on center stand) set your meter to DC Volts and place your probes on the battery terminals. Measure voltage at idle, then rev the engine, voltage should go up to about 14.6 volts DC but shouldn't go much higher.