Hi,
Thank you for the details, it helps a lot!
You may have accidentally changed the link colors to white, you can change that here:
If you wish to search PDF file contents, please check this documentation, it will help the proper setup.
PDF thumbnails are not possible in WordPress, it requires a properly configured Imagick, Imagemagick and Ghostscript library on your back-end server, and even in that case it may not work.
We will try to come up with a simpler solution in a future release, but it is greatly limited by PHP and WordPress, so some server side adjustments will be required even then.