So I replaced my CDI and now my battery is charging again.
Looks like the 2001 and newer shop manual supplement is missing the charging circuit troubleshooting process. So here is my take:
1. Check the main fuse - there is only one 20a fuse (the other is a spare) located under the right side cover.
2. Check the battery
3. Check the charging voltage at the battery - Should be 14 - 15 volts at about 5000 rpm
- If the voltage is wrong, replace the CDI
4. Check charging coil resistance test - Should be about 800 ohms
In the end, my CDI and rectifier were faulty. Coil was fine (of course, replacing the rectifier and CDI is a 5 minute job that doesn't require tools - coil was a 90 minute job that requires draining all the oil!)