Basil - most of the reg's I have worked with over the years, especially the Kawasaki ones, have a consistent colour-coding...
Black w/yellow tag (stripe) - earth.
White - regulated +12V direct to battery for charging
Brown - regulated +12v direct to wiring harness, not battery. Brown is a common +12v 'main' wire for heaps of kawasaki looms.
Yellow - not sure about this one. Its probably another +12v feed for a special purpose on your model.
I will check the wiring diagram for your bike - and the aftermarket regulator you got - was there no wiring diagram supplied with it ??
Here is the link to a 2004 ZX6R - it looks like the yellow wire from you OEM regulator, runs up to a 'junction box' - NFI what this is on your specific model....
http://www.mediafire.com/?f6roovjl7avIts about 39 meg, and is the full parts/wiring manual for the '04 model - I doubt there would be too many differences between your 03 and this one ...