Wow, I can't wait to read what you're going to put together.
For backround characters and civilians, I like to use Cantina Aliens (i.e. Walrusman, Snaggletooth, Myo) Jabba's Palace People (i.e. Barada, Ephant Mon, Skiff LAndo with Helmet on) Bounty Hunters (Bossk, Aurra Sing, Dengar, the Fetts) and other characters (Cloud Car Pilot, Lobot, Jawas and Ewoks)
I can't really help you with names, since I'm not too good with coming up with those.
What is the size of your Separatist army, since the 501st will need something/someone to fight.
Your gunship should come in handy, since it can fit in during the whole Clone War. You may want to invest into a Revenge of the Sith Jedi Fighter, since that would help for later in the Clone Wars. Good luck!!!