Then what is the Route you are taking to INPUT the documents.
Are you saying you Cant merge JPG files.. It aint hard..
As you say, it has Flaws(PDF), and unless they Clean it up, it will incorporate then into the file.
EPS, REALLY sucks, unless you clean it up.
If you are scanning the Docs, into PDF then its STILL a graphic, and STILL time consuming. Unless PDF will sort out the txt format, and then WHY not use it with another format.
The only reason for PDF is for copyright, and protection.