| Not 100% on the specific colours, but here goes................
There are three basic inputs/outputs on the regulator.
AC voltage input. This is from your engine. Usually two or three yellow wires depending on your alternator.
DC voltage output. This is the feed to the bikes electrics and charging system.
The last connection is for the warning light, if you have one.
The first two sets of wires are usually a lot thicker than the last set, due to the current they carry.
I'd guess the new rectifier was needed because of the three phase output of the later engine. It is more than likely that the some/all of the colour coding changed on the rest of the wiring two??
As I don't think the Monster has a warning light, I'd guess the wires you have left are the DC output. Red/white +tve and the green -tve.
I couldn't be sure though. There is usually a wiring diagram in the handbook. If you have the original with the early wiring in you should be able to download a later one of Ducati.com? | 
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