The two "must read" documents I would recommend here are LEED's Minimum Program Requirements, discussed on this LEEDuser page, and the LEED Rating
System Selection Policy
 . Mainly the first
one.
1) Seems like functionally this will be one building when
complete, so should be certified as one complete building. You can
pro-rate the renovation/existing building situation so that you won't be
so penalized on the energy side.
2) Seems like the existing
building can be ignored here, but check the MPRs to make sure you agree.