The lucene indexer indexes all objects and searchable attributes, regardless of section. So you should be able to search all sections, <b>provided the current logged in user has access to them (check this first in the roles/policies)</b>. Access control is done at search time.
You may try the admin interface and log in as admin to test.
In the search box specify
m_section_id:2
This should list all objects in the section 2 (which is by default the users section). Check your install if section id 2 corresponds to this or if you have other dedicated sections for users.
Which version of ez publish are you running? There are bugs in the advanced search anyway and a few search types are not yet supported by the lucene plugin (I hope to add these this week, together with patches for the advanced search).
About pdf indexing and other binary files: the lucene plugin relies on the ez publish configuration for this. If it works with the ez search it will work with the lucene plugin as well.