I rely on simple copy and paste onto a word doc, then save as RTF and convert into MOBI (I have a Kindle) using Calibre. I always convert PDFs in Calbre to MOBI and if I hate the way it looks on my Kindle then I convert the PDF to RTF then go in and edit the new RTF and convert that to MOBI.

I haven't used FLAG but when I use Fanfic downloader I get fed up with author comments between chapters, so for me I'll stick with copy and paste, I get a cleaner ebook that way.