My regulator/rectifier passes the continuity tests for forward and reverse bias but when I put it on the bench and hook it to a battery it shorts (blows fuse).

Just to clarify, connecting the red wire of the regulator/rectifier to a positive battery terminal and the black to the negative battery terminal should not cause a short circuit, right?

Rich, not sure where you are finding this red & black wire.

From your 11/19/20 post "The red and black wire doesn't connect to anything."

The regulator has three yellow wires from the three  phases of the alternator stator.  It has a black & white wire that ties to ground.  It has a red wire that ties to battery + via the fuse.  It has an orange & white wire that gets tied to battery + when the switch is on.

I suspect that if you have an internal problem with the regulator the fuse would blow as soon as you connect the plug to the regulator, because the the hot wire (red) has no switch to interrupt the current.

Does your fuse blow as soon as you connect the regulator, or do you have to turn on the switch in order to get the fuse to blow?   Or do you have to run the engine to get the fuse to blow?

Have you checked continuity across the red wire and the black wire.  The stock regulator should have 7.5 7500 ohms when meter positive is connected to red and negative to black & white.  When the meter leads are reversed it should read infinity.  I believe you checked this.  Do I have that right?  (11/21/20  Oooops!
Corrected ohms spec to 7500.  Sorry, my bad)

All three of the regulator yellow wires should read infinity when the meter leads are connected across any two, regardless of polarity (y1 to y2, y1 to y3, y2 to y3).

Have you checked insulation resistance to ground through the regulator housing?

Have you tried leaving the yellow wires disconnected to verify that there isn't some sort of shorted path to ground through the stator?  Try leaving the yellow wires disconnected and see if the fuse blows, then connect the yellow wires and see if the fuse blows.

Yes, I understand that he has an aftermarket regulator and that it doesn't have the orange & white (orange with white trace) wire, but what does he mean by "The red and black wire doesn't connect to anything."?

He defines it as a single "wire" (not plural).  Is he talking about a red wire with a black trace or is he talking about two wires, and why is/are the wire/s not connected to anything?  

As he describes the problem, sounds like he is wiring it up on a bench and when he connects red wire and black wire to a battery it blows a fuse he has installed in the test circuit.  The hot wire (red) and ground wire (black) should be polarity sensitive.  I now see in my manual that the resistance values are K ohms so a stock regulator should read 7500 ohms (+ to red, - to black/white) and infinity (- to red, +  to black/white).  I think his aftermarket units should be close to that to prevent the battery from draining through the regulator when the bike is at rest.

He says it "passes the continuity tests for forward and reverse bias".  Rich, please tell us more about how you did that test and what values you recorded.