It sounds as though you have heat-induced high resistance or even a heat-induced open circuit somewhere in the charging system; the problem doesn't appear until the components have warmed up and the resistance rises. I would double check all of your grounds and connections, especially those around the voltage rectifier/regulator.
Also, was the bike warmed up fully when you drew 50 AC volts per stator lead? If memory serves, your bike should generate approximately 260 watts at 5,000 rpm, so you should be seeing roughly 65 volts per stator lead on your bike; that puts you roughly 30 percent down from spec.