I'm withholding judgement on Deathtroopers until I actually read it... :/
A large part of Fate of the Jedi is about Luke and his son Ben investigating certain events of Legacy of the Force, and trying to better explain what happened. You'd be missing out on some fairly significant backstory if you skipped LotF. Even if I wasn't happy with some of the directions the plot took, it's probably worth reading. Apart from anything else, FotJ is still in the process of being written - if you get into it now you'll be stuck waiting months and months between releases. Just be warned that Karen Traviss is kind of in love with Boba Fett, so in LotF you'll see a lot of stuff about Mandalorians in every third book.
I don't know much about the Republic Commando video game, but there are four RC novels - again written by Karen Traviss, only the Mandalorian stuff actually deserves its place in a book about clone troopers with Mandalorian heritage. There are also two Imperial Commando books that haven't been released yet. I think there were going to be more, but Traviss has decided to leave the EU basically because Lucas insists on screwing over existing EU canon with the Clone Wars kiddie TV show.
Hope your Rogue Squadron comics turn up - a lot of my Star Wars comics have been 'misplaced' by younger brothers who do not understand proper respect for Star Wars, and had to be replaced :/ The Omnibus collections make that pretty easy, though. Re the Thrawn trilogy, couldn't you ask a bookstore to order it in? Or just buy online? I thought the internet had made the days of driving around in search of obscure books obsolete