I love having you around, Var.
Has a great deal to do with your writing style, I think.
Your problem is the transition. You have had habits and a social structure ingrained into you during some prime developmental years, and now you aren't living with that any more. Like you didn't know any of that. Gimmie a Captain Obvious pin or something. The remainder here is just brainstorming and may have no validity whatsoever, so it oughta be worth what you paid me for it...
There's plenty here that DO know from experience, too, but I gotta TRY. Sigh.
You
will adapt. It's something humans do very well. How you adapt is up to you. Maybe you want to take things slow, and change a little bit at a time rather than have this big huge "transform into civvy" thing going. Some you can't help, obviously, but decisions about your clothes or hair or vacation, for example, you could take a "what if this were a covert operation" p.o.v. and just work on something that blends in. Or, if there's a decision to be made, how would you tell a green private to handle the situation? Or what would you be told by your CO if HE had to decide?
Over time you won't need that sort of mental exercise but it might help for a while. I imagine the deference thing will pass as you develop the new working relationship with your coworkers and unit. I'm really surprised at the reaction to the "chain of command" question; that's pretty basic even if you've had no direct military exposure. This dude works with military folks all the time. In corporation-speak, though, what you're looking for is the "org chart."
Rogue said to tell you that her uncle is a veteran Marine pilot from the Korean War, and he still feels most comfortable in a buzz. But then, I've never served, and so do I.