I don't think there is an easy solution.
I know a software called Style Report from Inet Software. It is a Java package aiming at report designing for PDF format. Using this package, a PDF file is sliced into elements and described in XML format.
I am wondering if your company can buy this package. Then, you can use it to create servlets. In the servlets, you keep two copies of data and compare them... Once some data is no longer needed for comparison, you may save it to Oracle (this can be done in a separate Thread if it takes a long time.) This is only a rough idea. In any case, I suggest cashing some data in the memory. Frequet reading from Oracle should be avoided.
Hope some other guys can contribute..