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The BMW boxers aren't terribly efficient. Also note that they build up a lot of heat and need excellent airflow. They will overheat and suffer in really bad traffic and you can't leave them idling for very long. Also, it might be taller than you think - the cylinders are flat, but the crankcase design is actually fairly tall.
Bike engines in general aren't very efficient at all. Also think about the drivetrain and how you'll connect the engine to the wheels. The BMW engine is sort of like a cage engine - it has a big flywheel and dry clutch off the back and separate transmission.
The most efficient bike engine I've used I think is the suzuki Banidt 1250 motor. It also has loads of torque. It returned a consistent 50-60mpg pushing the heavily loaded bandit around with vigor. Being liquid cooled it'll be easy to keep cool in the cage configuration. It uses an integrated transmission with the engine and has a very large-diameter wet clutch that I think would hold up to getting a cage rolling more easily than most dry clutch systems. Its also a 10-minute job to replace the clutch plates rather than a 10+ hour job like on the BMW.
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