Raised gearing and a slow turn throttle (or a more controlled right wrist) are probably about all you can hope to do with/to the stock engine.
Aerodynamics are probably the best place to spend money on a motorcycle if you want to increase FE/speed for a given HP. Aero are largely bolt on/bolt off and doesn't involve the inside of the engine. Plus, unless you are a porting/engine guru with an extensive workshopyou probably aren't going to be able to improve the FE of many engines.
What you can do is reduce the demands on the engine power.
I can't think of many Ducati engines that have been designed for FE, and I've owned and raced a variety of (older) Duc singles and twins.
cheers,
Michael
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