Red/white is the output, and should go straight to the battery. Black is ground, I think (Kawasaki colors are unfamiliar to me). The other wire is switched ignition +12V, this powers the regulator section.
Wiring diagrams for bikes using this reg/rect are here
http://kz.mbsween.com/manual.htmlPossibly if you leave the regulator power sire disconnected it will act like a simple rectifier, I don't know. It's not a good idea to have two different regulators hooked up in my opinion.
The 400 has a barely adequate alternator and messing with the charging circuit like this is not a good idea. The Kawi regulator is for a permanent magnet alternator. The Honda one is an induced field type. In theory you could skip the Honda regulator by connecting the white wire at the regulator directly to the black wire, giving maximum output all the time. This might overheat the field coil itself, never tried it for a long time personally. If the Kawi regulator is working properly you should get a stable 14.5V at riding RPM with a fully charged battery.
I would still recommend using a rectifier and the stock regulator (if it's working OK). You can make a replacement rectifier quite cheaply using commodity diode bridges, instructions are in these archives.