I chose a sort of different approach. I modified the agent in the help documentation that goes for every notes item in all documents of a database and tests for the type, then built/updated a view then I basically exported to csv. As for the files, I just wrote them to disk by creating folders with the form name and within it put the folders with UNID's and inside all the attachments pertaining to the doc.
Although I was able to fetch all attachments, I did find it ambiguous to understand the main difference of the whereabouts of all embedded objects.
Another thing one has to keep in mind in a Java agent is that in order to not run out of memory one has to recycle what you are no longer needing.