Yup! its a problem to run the small battery on the older FI ducs. The newer ducs have a 550watt charging system, while the older stuff seems to be in the 250 watt range. If you figure that your injectors (@ 12-16 ohms) use 1 amp each at 90% duty cycle, your fuel pump is 3-5 amps depending on the dirtiness of the fuel filter, the ignition uses another 2 amps, the ecu uses 3 amps, your gages 2 amps. So, you may only have an extra 70 watts to charge the battery @ PEAK output... drop below 6000rpm and your at less than peak.

Pay attention to the phase of charging system. Ducati changed from 2 phase to 3 phase in the late 1990's.