Thought this was interesting, from an official Pagani statement:

Click here to enlarge Originally Posted by Pagani
The engine of the Pagani C9 is not a derivative of the AMG V-12 engine developed for the SL65 Black Series, nor is the AMG V-12 engine in the SL65 Black Series derived from the engine AMG is currently developing for the Pagani C9.

The cars are very different in their character and conception and the engine will reflect this in its technical characteristics and behavior.

The engine in the Pagani C9 has been developed specifically for that application by Mercedes-AMG GmbH.
Specs are 6.0 liters and around 700 hp at the moment.