AA has an interline e-ticketing agreement with FJ:

http://www.aa.com/content/agency/Boo...g%20Agreements

But as this is an AF ticket and AF has no such agreement anymore (at least for interlined baggage), would AA be in a position to check my bags all the way though to NAN in the absence of an interline agreement between AF and FJ when the ticket is, in fact, an AF ticket, and not an AA ticket?

AF no longer will handle FJ's bags, etc.:

http://www.flyertalk.com/forum/showthread.php?t=769810

NH may still do so:

http://www.flyertalk.com/forums/showthread.php?t=748075