AO3 story URLs don't contain a title or anything that changes. So unless you managed to remove the identifiers:url metadata from the Calibre books, it should have found them. Unless you had selected FFF's 'Add Book' mode for some reason. FFF also has an option to match by title/author.
As for "FanFicFare doesn't recognize chapters..." that is almost always caused by editing the epubs with some other tool that restructures the epub, or breaks FFF's hidden metadata.
An alternative would if you have a chapter_start setting that doesn't include the hidden <meta> tags correctly.
If you post one of the "doesn't recognize chapters" epubs, I can probably tell you which. SFW please.
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