When uploading PDFs for a PCT, do the specification, claims, and drawings all have to be loaded individually or can they be put into one file?

Other than when submitting a PCT-EASY zip file, which includes the Request and Fee Sheet, you will generally file a PCT Application like you would file a utility application via EFS-Web. Therefore, you have the option of attaching these files as individual files or as single multi-part files.

USPTO FAQ - Questions and Answers (2007JUN01)