If I were going to attempt this, I would put them on either side of the voltage requlator, just in front of the battery. It will be a tight fit, but might work. I would then put a deflector plate below it to keep the spray from the front wheel. The ST has such a deflector plate. Then I would go through all of your connectors and give them a good cleaning, and a liberal dose of silicone dielectric grease. It helps keep the weather out, and connectors working well.
While you are at it, I highly recomend some new coils. the high tension leads are not replaceable on the stock coils and are a common source of failure of the ignition system. The Dyna Coils are the common upgrade, although not cheap. ($200) Ca cycle works has a nice kit with some nice wires already attached.
http://www.ca-cycleworks.com/ I put them on my bike for a noticable improvement. Stock coils are 4 ohm, which is almost impossible to find. After market are generally 3 ohm. You could also find some stock Ducati coils for cheap on e-bay, and they are much smaller.
Cheers,