Project boundary issues

I am doing a project in Lahore, Pakistan for the British Council. It is a 6,000sf library located on a 50,000sf site. The site has two entrances flanked by guard rooms, a prayer area, storage spaces and a main building covering an area of 15,000sf. We have registered the project with a site area of 29,000sf which includes all areas effected by construction. Now I realize the area defined in the site is not reasonable, a corner of the site in not included so as to keep prayer area out of LEED boundary, all parking is included but it has more parking stall than required by credit 4.4, the entrances are common so at places the LEED boundary hugs the main building which is again quite odd. I was thinking of registering site first and taking the campus approach but the client is disagreeable on spending more money on project registrations. I want some advice on how proceed with redefining the project boundary.