most efficient pipeline for rendering large documents in after effects
I believe that using pngs from the pdf is the best compromise between quality and speed. Your main concern being the render-time? If so, (I am sure you have, but just to be sure) have you checked if you're using Hardware-acceleration? You should also purge your cache frequently and have both the footage as well as your cache-directory as well as the project files on a fast medium, like an ssd.

I'm not certain with how familiar you are with those standard optimization techniques, so I'm just throwing this out there. If there's a different problem, please elaborate.