We use a service called ChimpKey - It is a very flexible service that allows you to convert your PDF documents into clean EDI (XML,X.12,csv etc). After the initial setup which was very quick and easy, we now email our documents in and get XML back and loaded into our ERP in a couple minutes. I wish I had known about ChimpKey years ago!
Here is a link if you want to see more http://chimpkey.com