Personally, I'd go C, A, because Shipwrights (And it's Hephaestos, I think) build ships, and it sounds like you want a research group as opposed to a builder. Also, going with a fusion of two pre-existing names (option B) means you're in some ways limited by the already existing info about those two companies, and you can't allow your writers imagination to flourish to it's full extent.
Option A for the second category is my choice simply because ease of pronounciation = ease of association for the player. Plus, if you ever get them, your voice actors would love you from the bottom of their hearts (try saying Themotheus out loud without thaying Themotheuth a few timeth)