This question is now old, and there are no longer any PDFs linked on http://cs.uic.edu/~asmirnov/publications.html, so I'll skip the first set of questions. It is no longer possible to review your setup.
But I'll answer your three "other questions":
Every PDF handed to Google Scholar must be a single paper. Submitting a whole issue as a single PDF-file is not accepted. Quoting from the Google Scholar Inclusion Guidelines for Webmasters:
"Place each article and each abstract in a separate HTML or PDF file. At this time, we're unable to effectively index multiple abstracts on the same webpage or multiple papers in the same PDF file. Likewise, we're unable to index different sections of the same paper in different files. Each paper must have its own unique URL in order for it to be included in Google Scholar."
Google Scholar will scrape your PDF for meta-data. So just linking to a full text PDF of a single paper will work if its format follow certain "conventions". See the section "Indexing of content without the meta-tags" in the Google Scholar Inclusion Guidelines for Webmasters for details about these "conventions".
However, for better control over the meta-data, it is recommended that you supply a HTML abstract with meta-tags along with the full text PDF. For a link to the Google Scholar guidelines for this file, see the section "Configuring the meta-tags " in the same document.
Google Scholar prefer sites to export meta-data through HTML abstract files with meta-data embedded as meta-tags. What tags to use and how to embed them are described in the Google Scholar Inclusion Guidelines for Webmasters.