Automated Blender Import/Export

Hello : ]

I’m new here so feel free to move this thread if its wrong here…
I need some tipps on how to design automated import/export.

Im currently working on an open source java app which needs to be able to automatically convert 3d meshes from a special 3ds file format to another special JSON file format. I have Blender Import/Export plugins available for both file formats.

Is there a sepcific api documentation (haven’t found import/export/plugins in blender api), examples or tutorials in regard to calling those plugins from a python script, which in turn would then be called by my java code?
I also need to be able to change blender user preferences (the preferences are expanded by one of the scripts) and select options in the import/export dialogs of the used plugins. I also need to be able to set the file locations from/to where the meshes are imported/exported.
Also performance may be interesting as i need to convert up to 1000 meshes at once when the user calls a function from my java app.

More links for anyone interested in what im actually trying to do:

Project for which i develop the application: Gothic Reloaded Mod
GitHub page for the application im developing: Gothic Mod Manager
Plugin for import:Gothic Kerrax Importer
Plugin for export:Three.js Blender Import/Export

I should probably also point out ive never programmed in python before, but writing a small amount of python code should really be a no-brainer after looking at some tutorial/example code.

I appreciate any tipps, links, suggestions or questions : ]