Thank you for your feedback on the import process, @ajn. I’ve passed it on to the team.
When importing PDFs, you should observe the progress of the Google sync, and you need to check Google Drive for the files.
Points 2 and 3 are addressed in the new Paperpile, available in private beta. Some of the new features for label management include renaming labels and folders via search and replace, merging labels, deleting multiple labels and folders at once, and changing color of labels in bulk. You can also update multiple references at the same time (e.g. change the same field for all chapters in one book).