If you have a functional iServer IDAPI is the only way to go here. You should be able to build a pretty simple client to log into the volume and traverse the virtual file system. For each report you encounter you can execute the report with an output type of PDF and a spot to land the output on the file system.
This thread at BIRT Exchange has a lot of what you need. right down to executing a report design via IDAPI and requesting the output to be in PDF format.
Do you have the IDAPI API guide? If so just point Eclipse at the WSDL and you should be good to go.
Good Luck!