It certainly doesn't sound good, but I can't see how the crank/generator can have broken/come loose, as even though it makes a duff noise it still runs, (badly), seeing as the ignition pick up is on the generator rotor if that wasn't spinning the motor wouldn't run at all.
The thing that concerns me is that there was no, or at least very little, oil in it when you changed it again. That's not going to have done the bearings any good at all, however if it seems OK under three thousand RPM there is room for a certain, (limited), amount of optimism, it could just be something loose.
Despite being your only transport, I really must advise that you don't ride it until it's been checked by someone who will be able to make a reasoned diagnosis of what's amiss.
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If an SV650 has a flat tyre in the forest and no-one is there to blow it up, how long will it be 'til someone posts that the reg/rec is duff and the world will end unless a CBR unit is fitted? A little bit of knowledge = a dangerous thing.
"a deathless anthem of nuclear-strength romantic angst"
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