Do not copy the files to your Kobo. Place the install.ps1 script and the .zip file in the same directory on your computer. Run the script from there. What you are currently seeing is every file that your Kobo scanned and added to the database since you did not add the exclusions to the Kobo eReader.conf file.
To quote the first 2 steps in the instructions in message #2 in this thread:
Windows:- Check the previous message, and download the ZIP package that you're interested in.
- Download the Windows install script, in the same folder.
Once you have done the install, safely eject your Kobo. At this point, the files that were previously imported will be removed and deleted.
So connect your Kobo and run the install script again to copy the missing files back.