Hello everybody!  Let me first preface this question by asserting that I am an idiot.  With that now out of the way...

I tried to jump start my dead battery with the leads connected from a car to the motorcycle... except, on the motorcycle, black was connected to positive and red was connected to negative.  (In my defense, there was a black cover over the positive lead, but anyhow...)  Naturally, this just shorted out the car battery.  Then I did something even more stupid and turned on the car engine and tried this...  of course this caused yet another (even worse) short.  Then I did the most stupid thing of all and tried connecting this to the ground terminal of the battery with the black cover (which was actually positive).  

This is when my headlights wouldn't light up anymore.  Fortunately, I had learned, that I blew a fuse.  I replaced it, got the bike started, then quickly noted that the charging system no longer worked.  

I tested this with a multimeter hooked at the battery terminals, reading only 12 volts at 5000rpm (should be 14-15V).  Also, I verified the stator-alternator leads (hooking up to the voltage regulator) had continuity between all 3 leads.  

Anyone have any idea why my bike will not charge anymore?  

Thanks.  

I think you are going to be looking for a new voltage regulator. Count yourself lucky the motorcycle still runs, because that means you didn't destroy the ignition box as well. Solid-state stuff usually takes umbrage at reversed voltage.

Ok, so I acquired a known and working voltage regulator-rectifier.  The problem still persists: the battery does not charge itself.  

At ~5000 RPM voltage across the battery terminals still reads a little over 12V.  Also, the batter does retain *some* charge because the headlight remains powered for a while after the motorcycle is jumped from a working battery.  

Any ideas?

Thanks