Is it possible that when you ride the bike in the morning and then park it you are leaving the ignition in the second position, the one that leaves the parking light on? Or that your voltmeter is drawing current all the time? I put a Wudo 90S fairing on my bike with a clock and voltmeter, using the factory harness, and the battery seemed to drain overnight. Took it off and the problem stopped. Not a lot of room under that ignition switch for all the connectors. On my 83 US spec R65, when the bars are fully turned to the left, the turn signal switch hits the tank bag just enough to turn it on, and that will drain the battery. You might try systematically unplugging lights, one at a time, to see if you can isolate the drain. I think if the alternator wasn't charging you would have a red light on. Could be as simple as a multi pin connector loose or corroded. A wire to one of my turn indicators wore through the insulation and was grounding to the mount. After a while, the fuse would blow, but not instantly, which was irritating. After I found the fault it was so obvious.
Electrical gremilns are maddening...