1. Back up affiliated directories and possibility to restore them to given folder.
I'm not really sure what you mean by "affiliated" directories. But the FEBE user-defined backup feature does allow you to specify any directory (or individual file) for backup/restore. The restore, however, is always applied to the original directory path.
2. Substitution of preference values from windows paths to unix pathes and vice versa within restore.
I've toyed with this idea before, but decided it wasn't really practical. For instance, my cookies are stored in "C:\Users\CBaker\AppData\Roaming\Mozilla\Firefox\Profiles\0yimjvq0.Chuck(Fx3)\cookies.sqlite" on my Vista box and "/home/chuck/mozilla/firefox/h3oui48c.Chuck/cookies.sqlite" on the Ubuntu box. How would I automatically convert this path into the corresponding *nix path?