Interesting looking project. In my opinion, though, you are trying to do too much in a single drawing and have exploded too many blocks. That said, there are several approaches that will work:
1)Use qselect. Choose block refererences. Choose Select All. Choose Exclude from new selection set. Choose OK. Execute the flatten command on that list. Then qselect, choose block references. Choose Select All. Choose Include in new selection set. Choose OK. In the properties palette, set the z elevation coordinate to 0.
2)Repeatedly qselect by object type, selecting all. Then choose the appropriate (z coordinate, elevation, etc.) in the property palette and set to 0. If an object type doesn't have a elevation or z property, use the flatten on that selection.
Architect, Registered NC, VA, SC, & GA.