Here is a nice example database to show how to make clicks on a PDF:
So first we render PDF to an image using DynaPDF functions. Than user can click on image inside a container to set a point. We draw the point with our GraphicsMagick functions in MBS Plugin and build a list of records for the points.
Later those points could be used to draw them on a new PDF with existing PDF in background.
Maybe this is useful for you? I'll include it with next plugins (or email me for a copy)