Here's a link to the charging guide on the site here. It will show you how to test everything. You've done some of the tests already. There is a simple one to check your regulator. But, the amount of change in your charging output (about 2 volts) seems about right, the starting and finishing numbers are just too low. It's possible the rectifier portion of your combined reg/rec has gone bad ......
http://www.xs650.com/threads/expanded-charging-system-guide-in-progress.10561/
These bikes use 3 phase alternators. There are 3 sets of windings or coils in them. You have 3 white wires coming out of the alternator. One white connects to each coil. These run to a 3 phase rectifier. That changes the AC output from the alternator to DC current for the bike. The rectifier has 3 sets of diodes in it, one connects to each white wire/alternator coil. If one of those diodes has gone bad, you will only get about 2/3 of the output from the alternator because it's only running off 2 of it's 3 coils. This may be your problem. It's also possible one of those coils in the alternator itself has gone bad.
So, I would test your regulator, rectifier, and alternator. I think you'll find your problem there, most likely in the rectifier or alternator. Hope for the rectifier. That can be replaced with a separate, stand alone unit for less than $10.