Hi,
I have already completed projects with all of the component parts of your requirements.
PDF upload is fairly standard.
For the PDF to jpeg conversion I will use ghostscript which is free linux software.
You will need linux hosting with ghostscript installed for this to work, I can install for you if you have a VPS not a cheap shared host(may be installed already).
Then javascript to draw and record the coordinates, ajax to send to the server and PHP to save in your database.
Mark