After hours and hours of banging my head against the wall trying to find a fix for this stutter problem, I believe I have finally found the solution...
To fix the stutter completely
1. In the Nvidia Control Panel you must set the Far Cry 3 specific settings (under Program Settings) to force Vsync Off.
2. Install Geforce Experience (http://www.geforce.com/drivers/geforce-experience) and use the "optimise game" option.
I used to have the worst video stutter and now it is completely gone.