How to create a standard firm wide pdf template?

Hey! I work for a tax firm and I was wondering if there was a way to program a standardized bookmarked pdf to consolidate client documents for tax returns when they are scanned in?

These bookmarked pdfs would need to follow certain conventions in how certain scanned documents are arranged. If possible I would like to have certain document data be recognized and categorized from the scan job automatically. I have no idea if this would need third party software to be paired with acrobat or not in order for that to happen.

My end goal is to have client data come in, it be scanned in and the resulting pdf would follow the structure of the tax forms. W-2s being the first bookmark, then brokerage statements being the next bookmark, etc. Additionally the first page of this pdf needs to have a document attachment for both a  preprogrammed excel file and a blank word doc for missing items and note taking. Said excel and word document needs to keep their unique data within the pdf file. I do not want one excel or word doc attached in one pdf file to be shared with another pdf file as the items and notes are client specific so they need to stay within their respective files. 

I know this is very complicated and it is rather hard to explain so if anyone has any recommendations on who or what I need to consult to start building and programming these templates and conventions out that that would be great!