Hello Mike,  Euro Motoelectrics sells Rick Jones book “Classic Boxer Charging”.  It’s a great little book that walks through diagnosing charging issues. Seems like most airhead owners wind up having one of these books. EME gets $30 for it, but I think it’s worth it. 

My check list...

1) Battery. As you noted, batteries may seem OK coming out of storage, but unless they were pampered over the winter then there is always the chance. My test is this: charge the battery slowly for 24 hours, remove the charger, turn ON the headlamp for 1 minute, then use a voltmeter to get a Voltage reading across the + and - terminals. This reading MUST be above 12.2 volts. If you see a reading like 11.8V or even 12.0V, then that battery is gone. An optimal battery should be 12.3V or higher. 

And as always, check the battery connections for terminal corrosion at BOTH ends of BOTH cables. I highly prefer the new, sealed, AGM batteries because they don't leak acid, which reduces corrosion issues at the battery terminals. 

2) Brushes. Replace the alternator brushes. The length of the carbon decreases over time, which in turn decreases the spring pressure against the slip rings. Poor brush pressure equals poor connectivity. 

3) Voltage Regulator. Replace the worn-out, 50yo, OEM mechanical voltage regulator with a modern solid state device (which has no moving parts to break or come out of adjustment). If you don't want to buy the one from Motorrad Eliktrik, then Here's One on EBay set up for AGM's for $24.

Hope this helps.