I prefer MongoDB due to own experience with migration of old archive of pdf and meta-data to a new “archive”. The biggest advantage is speed of filters output - a new archive is way faster and reliable then the old one - but also the the easy programming of MongoDB with many code snippets and examples available. I have no personal experience so far with Couchbase. From the architecture point of view both options are OK - go for the one you like.

I would like to suggest MongoDB or ArangoDB (can't choose both, so ArangoDB). MongoDB is more mature, but ArangoDB is more interesting if you will need to bring graph database ideas to solution. For example if some data or some documents are interlinked, then probably ArangoDB is a best solution.

To process tables we used Abbyy software stack. It's great on table extraction.

If you can select text with mouse drag in PDF. Use pdftotext it is fast! You can install it on server with command "apt-get install poppler-utils". Use it like "pdftotext -layout /path-to-your-file". In same folder it will make text file with line by line content. There is few classes on git stacks that you can use, also.