Pdfmod is very simple and powerful tool to add (as bookmarks) an outline (structure) to a pdf.
automatic crop pdf margins
I found this excellent tool: PdfCropMargins, a very light app (both for Linux and Windows), which can crop automatically pdf white margins (top,bottom,left,right) even if they are very irregular (different from page to page). With a great accuracy. And without growing the pdf size.
You can use the gui, starting from a command line, such as pdf-crop-margins -gui “original-pdf.pdf” -o “target-pdf.pdf”.
save only some pdf pages from a pdf
You can use Okular, of course: print to file -> the pages you want. But thus you get an image pdf. If you want keep a text pdf, you can use a program like PdfArranger, which allows to save (only) the pages you want from a whole pdf, keeping them as searchable pdf (text).
syncing subtitles troubles
framerate
Correcting subtitles framerate may be very important to sync it with audio/video. You can select all subtitles with an editor, and change framerate (for example to 25 from 23.976).
Thereby you should see the video correctly (with VLC or others).
the ultimate solution
If adjusting framerate didn’t fix your problem, you can try an excellent tool (for Linux, Windows and Mac as well): SubSync, whicth works syncing audio with subtitles, and was able so far to solve all my sincing subtitles problems.
You could have a permissions problem working the first time with SubSync, but you will find easily on the web.