You would need to get a puch magneto as well since the "ducati" one dose not have the point actuating lobe.
I am only familiar with the wiring on my Korado but if you give me some more info I can probably either work out the correct way things should be wired or a work around.
From my understanding the bike that that engine originally hooked up to had a battery. There should be a small silver box with 2 or 3 hookups on it, it looks like it is filled with gelitan. That converts your engines ac power to dc current to charge the battery. Since the bike had a battery all the lights ran off that. Now that you don;t have a battery you need to jerry rig the wiring so your lights run on ac power.
If you have spark your wiring should be good. The green wire coming out of the engine should go to the verde G port on the Ducati CDI. The red wire should go to ground and the "stop" plug should go to your kill switch. If that wire is grounded your engine will stop.
The yellow wire coming off your engine is the power for your lights. just run that directly to whatever lights you have on the bike ( I run it to only the headlight).
If you have other wires coming off your engine you can just ground them. Some of those wires might be carrying 6v current and later on down the road you could use those as tail/brake light power.
And yes it I get the opportunity I will talk your ear off.
Shoot my a email if you need anything else paz.chris at gmail.com