When I drag several pages from a Finder folder into PdfClerk’s page list, the page order is scrambled (they were sorted by name in the original folder). When I’ve dragged 60 pages, it’s quite a task to get them back into the correct order.

Unfortunately, the order in which Files from the finder are handed to PDFClerk for import is not necessarily the same as the sequence in which they are listed in the Finder view you drag them from. PDFClerk imports the files in the order they are provided, so it is really dependent on the Finder’s whim.

There are however to things that may help you:
1. In the application preferences you have the option to import PDF files using their internal document title property (the default), or using their file name. If you are after alphabetical order you may have better results changing this setting to use the file name, if you are indeed importing PDF documents, and then:
2. If you need alphabetical sorting, you can sort on source name by clicking the table header of the second column in the page list.