Is this possible? I want to create a PDF from Photoshop while keeping on a master layer/group for all pages AND turning on/off invidual layers/smart object in another group? I know there may be a way to do this with Layer Comps but I would rather just use layers.
Please elaborate as your description seems unclear (to me at least).
What is the exact layer structure and what are the rules regarding showing and hiding the various elements?
Creating a multi-page pdf in one go from one psd-file is not a default option as far as I know, but one might be able to automate such a task with a Script.
With all your layers ready, File > Scripts > Export Layers to Files. Choose PDF as filetype. Choose location, give a filename prefix and hit OK. Your layers will be exported as individual PDF files with prefix_layername as filename to the chosen location.
Note that the output dimension will be the full canvas size (even if the layer only occupies a limited boundary).