We have covered your item 5) " ... display of MS Excel files ... " is a related support topic:
Interactive Excel Sheets
I know your project has moved on from the "PDFs viewed one at a time" idea, but I'm updating this topic because I ran across a solution during my work with another user.
The Easy Fancybox plugin supports the display of a PDF document in a pop-up shadowbox window.
To configure Easy Fancybox go to the Settings/Media screen. Check the "Media: [X] PDF" box. Uncheck the "PDF: [X] AutoDetect" box (unless you want every PDF on your site displayed this way).
If you uncheck the "AutoDetect" box, you can control which galleries display the pop-up shadowbox. Create a custom markup template (Settings/Media Library Assistant screen, MLS Gallery tab). In the “Item” section you can replace “[+link+]” with:
<a title="[+title+]" class="fancybox-pdf" href="[+link_url+]">[+thumbnail_content+]</a>
I have released MLA v1.40 which lets you add a class without a custom template; add
mla_link_attributes='class="fancybox-pdf"' to your
[mla_gallery] shortcode. NOTE: There is a small bug (which I will fix in the next release). If you use
mla_viewer=true to generate PDF thumbnails with the Google File Viewer, the
mla_link_attributes parameter is ignored. I the interim, the custom markup template works well.
I am marking this issue resolved, because there is no further MLA work to be done with regard to your project. Thanks for a stimulating discussion.