Why not connect through WiFi to get files? You can install an FTP server or use my WebPortal's FileManager to download/upload stuff from the reader through the PC-webbrowser
You can run stuff while the Kobo is connected to PC, my AutoShelf mod does that - while it's connected to PC you can enable/disable AutoShelf by touching the screen.
Getting the kobo browser to run while a PC connection is active may not be easy to achieve though
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