A continuous 12 months of energy data using Portfolio Manager is required for EAp2—we discuss details on that over there. I don't think it's necessary to wait to start this for EBOM registration.
Other performance periods must generally be at least 3 months. We just posted the video of a webinar that has some great tips on successful performance period management, and more detail on this. I recommend it.
http://www.leeduser.com/strategy/leed-ebom-eight-steps-success