I have 49 character keychains and have kept my records up to date.
From what I can see your missing, compared to my list) the just-released Watto and Anakin Skywalker (child) as well as the new Boba Fett, and the Clone Wars versions of the Emperor and Yoda.
I didn't get re-released keychains where they might have removed the LEGO tile or the carabiner-style ones. You mention a clone trooper with blue arms...this would've been the 2005 ROTS Clone Pilot as opposed to the yellow-striped 2011 Clone Wars Clone Pilot.
Several of these (Vader, Chewbacca, Stormtrooper, Yoda, R2-D2, and C-3PO) have been re-released with minor differences such that they are essentially undistinguishable, apart from Vader's chest. Have been hoping for a newer R2 with a revised dome as per the current mini-fig.
Hope this helps. I'll see if I can get a picture of these...keychains kept in a shadow box