Anything that isn't labeled as an optional rule or specifically disallowed in the faq is allowed right?
Yes, that's correct. For the most part, if it's published for SR4, it's legal. I think Bull said early in Season 4 that he intended not to saddle the Missions campaign with a ton of optional rules, and that he intended for the Missions campaign to be as true as possible to the SR4 line as a whole.
Two exceptions are the Way of the Adept and Way of the Samurai PDF books, which are labeled on the front cover as Option, so the whole of both are disallowed.