It can be frustrating to check a charging system without a known good battery, as a bad battery can make the charging system look faulty.
Charge the battery fully. The remove from charger and let it rest for 2 hours unconnected before measuring its voltage. It should be 12.6-12.8V in this condition.
Then start the engine (kick start is best here), and make a voltage chart showing the voltage reading at idle, 2000, 3000, 4000, and 5000 RPMs.
If you deplete the battery with electric start before hand, hold at 3000-4000 RPM for 15-30 seconds an watch the battery voltage change trends. The bike's charging system does not replenish a depleted batter quickly. In fact, it would take 10-ish hours above 3000 RPM to fully charge it from depleted.
If the charging system is weak, like a bad diode in the rectifier, or a bad leg of the yellow wire connections, removing the headlight fuse, will help charge a battery to peak.