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).
I think the OP wants to keep some elements visible in all resulting pdfs, so Export Layers to Files might not be a perfect fit.