Yes, I meant the bulk import -> search and replace. But I've never bulk imported myself, so I can't really help you if it doesn't work.

Re the "Title by author - Author.epub" -- is maybe the title tag in the meta info of the html set to "Title by author"? You might want to try removing that with the bulk import search and replace, too. It's going to fallback on filename for title, then, I think. If you convert one author folder at a time, you can just edit the author back in via bulk editing of meta tags.