I am wondering if I can set it up so that I convert the files I need, add tags and covers, move them to the location of my choice and then have Calibre delete the files and folders in its library created in the process.

I don't see why you couldn't do that. You'd have to manually copy the converted files to the location that you wanted one-by-one though as Calibre sets up a new file for each book. Deleting from Calibre afterwards would be as easy as selecting the books and clicking the delete button in Calibre.