I know little about newer bike electricals, but...
The 3 yellow wires must be the stator coils. Black is pretty much Honda's color for ignition power, but later models might have changed. Red is normally the battery connection. Green is usually ground to the rest of the world but I don't know for sure about Honda. So the mystery is twofold:
Is this a reg/rect for an induced field alternator? It might be for a unit with unregulated alternator, that regulates the output power with a pass transistor or using pulse width control. This is the more elegant solution to the Lucas zener diode "regulator".
If it IS for a field controlled alternator, the red wire is 99% likely to be the battery wire, so black and green wire remain and it might ground through the mounting bolts too. Probablybly the black wire is ignition power, allowing the regulator electronics to not use power when the key is off. Looking at the electrex replacement units they have a red, black, and YELLOW wire; maybe your green is field although nobody should use green for non-ground wire IMO.
You could experiment a bit and see. The red should show diode-like behavious to the (unconnected) yellow wires (an ohmeter will show low one way and high the other). If the yellow wires show the same sort of pattern to the mounting bolts then probably the unit grounds through them.. so it has to be screwed to the frame to work.
So, if the red is battery and ground is via the case: See if there's resistance from the black wire to ground. If there is - but not a low/short reading - then try it as ignition power. If it doesn't smoke or explode when switched on, see if the green wire has battery power on it. If so, connect the yellow wires and try connecting a cliplead from the alternator field wire directly to the battery + terminal and starting the engine - revving should drive the battery voltage above normal as the alternator is making 100% power. If the battery voltage goes above 14V or so and the green wire IS the field, the voltage on it should drop down to zero or a few volts. If that happens, you have it figured out and can connect green to field and try it out for real.