[DNSB]

I would suggest adding NickelMenu and adding USB Connect to it's menu. I've placed a sample config file in the spoiler below and attached it as well. Just copy the file config (no file extension) inside the .zip file to the /.adds/nm directory on your Kobo after installing NickelMenu. After safely ejecting, you should be able to use USB Connect to reconnect to your computer without needing to unplug/plug.

Spoiler:

# -------------------------------------------------------------------------------------------------#
#
menu_item : main    : Dark Mode           : nickel_setting : toggle : dark_mode
menu_item : main    : Screenshots         : nickel_setting : toggle : screenshots
menu_item : main    : Import books        : nickel_misc    : rescan_books_full
menu_item : main    : Toggle Auto USB     : nickel_setting : toggle : auto_usb_gadget
menu_item : main    : USB Connect         : nickel_misc    : force_usb_connection
menu_item : main     : Reboot             : power          : reboot
menu_item : main     : Shutdown           : power          : shutdown
#
# -------------------------------------------------------------------------------------------------#
#
menu_item : library : Dark Mode           : nickel_setting : toggle : dark_mode
menu_item : library : Screenshots         : nickel_setting : toggle : screenshots
menu_item : library : Import books        : nickel_misc    : rescan_books_full
menu_item : library : Toggle Auto USB     : nickel_setting : toggle : auto_usb_gadget
menu_item : library : USB Connect         : nickel_misc    : force_usb_connection
menu_item : library : Reboot              : power          : reboot
menu_item : library : Shutdown            : power          : shutdown
# -------------------------------------------------------------------------------------------------#
#
menu_item : reader  : Dark Mode          : nickel_setting  : toggle : dark_mode
menu_item : reader  : Reboot             : power           : reboot
menu_item : reader  : Shutdown           : power           : shutdown
# -------------------------------------------------------------------------------------------------#

As for PDFs? I just copy them to my Kobo from my calibre library. If you are not using calibre, just create a directory in the root of your Kobo's exposed storage and store the PDFs there. The only reason for the directory is that the root of a FAT32 partition has a limited number of directory entries and long filenames chew up that number like it was popcorn.