Tony, I think the place you need to start to answer this set of questions for your project is with LEED's Minimum Program Requirements. We have a guidance page on the MPRs here, and I think you would also get some perspective from this discussion about setting the site boundary.
It seems quite likely that your site boundary will need to include the entire building; thus this would be included in your energy model for LEED EAc1 and in all of your credit calculations.
Feel free to post back with follow-up thoughts or questions.