Pdfmod is very simple and powerful tool to add (as bookmarks) an outline (structure) to a pdf.
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”.
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).
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).