Try this http://dev.bukkit.org/bukkit-plugins/serversigns/ you can make commands for the signs.
Why not just use Group Manager for prefixes?
Also try upgrading to Citizens 2
I would use Group Manager instead, its way easier to use.
If you haven't tried BisectHosting I would definitely look at it! People may think they sponsor me because of how much I recommend them :p but...
I used to have the same problem, It just fixed itself some how
Separate names with a comma.