M&V baseline for retrofit?

Hi, we are working on a extensive renovation of a 80,000 SF university classroom/office building using LEED NC 2009. Most of the mechanical cooling will be removed and it will be restored to naturally ventilated with fan assist and nighttime dehumidification. I'm seeking clarification on what kind of modeling will meet the requirement for the baseline. This credit references IPMVP Volume III for New Construction in gathering a hypothetical baseline - one that, in other posts here, it was confirmed should also meet the "proposed case" in EAc1. However in our case the building has been extensively wired and many monitoring points put in. 12 months of ongoing data collection will cease next month and then the baseline and projected savings will be modeled on this. The draft M&V plan submitted by the consultant (not written specifically for LEED conformance) uses Option B and Option C. The model to be used does not appear to be tied to ASHRAE 90.1-2007/Appendix G or the EAc1 model. Is there still a way we can meet the requirements of this credit to receive 3 points? The IPMVP manual itself in chapter 2 does not specify how the baseline is to be calculated, but LEED does. Thanks!