New rotor installed, charging fine, no blown fuses, back in business as soon as the new chain and fuse block arrives. Thanks for all the help.
Is it a new rotor, or a used one? If it's original, you will face the same problem sooner than later. I hope you kept the old one and I'll get to that.
The issue with the alternator rotor is the insulation on the wires it's wound with. Wire insulation technology from 35 years ago was a very long way away from what it is now. Now that it's old, once exposed to heat and vibration, it breaks down very quickly and develops short circuits in the winding. Depending upon where the short is, you get 2, 3, or zero ohms. It won't make a strong enough magnetic field to induce current into the stator windings and your battery goes flat, right through the rotor with help from the voltage regulator. Yes, it can blow the main fuse.
If you send the old rotor to someone reputable for a rewind, the new wire has very much improved technology in the insulation.
Custom Rewind enjoys a good reputation for that. The rewound rotor will likely outlast the bike. You just have to keep in mind the brushes are a service item that you have to look after. The voltage regulator feeds battery current to the rotor through the brushes at a rate that depends upon the demands on the system. It's really quite sophisticated for a motorcycle at this price point.
Unlike the XS650, most motorcycles employ a PMA (permanent magnet alternator). Instead of a battery current fed rotor, the rotor is a permanent magnet with no wiring to it. The faster it spins in the alternator, the more current is induced into the stator, regardless what the demand is. That is why you see the big heat sink on the voltage regulator. The excess current has to go someplace, so it is dissipated as heat.
I met Hugh of Hugh's Handbuilt just recently. He told me he now has a PMA system complete with ignition. He was running it on an XS650B. I didn't ask the price, but I'm sure it could be a great option for many, especially as ignition parts become scarce.
http://www.hughshandbuilt.com/product/complete-xs650-cdi-system/
I hope this helps somebody, if only a little.