Hi Christopher,
The rules say that you're NOT allowed to use the LEED 2009 guidelines for which materials to include/exclude in an NC 2.2 project. To be safe you should just include the MF 2004 sections that correspond to the allowed MF 95 sections.
If you want to push this boundary you could submit a CIR or just include all the allow LEED 2009 sections and see how they review it, but I wouldn't count on that getting approved.