I wish that I could help you, but it's been too long since I was one the Alaska.
I do remember that we climbed underneath the turtledeck and could walk thru it hunched over a little bit. I'd say that the missile's could extend roughly around 4 feet above the main deck with the turtle above them of course. As for how far back it went...I remember climbing out of the aft escape trunk, moving a few feet aft and going back underneath it to "ease" the towed array into the guides on the port side. There was even less room here as this is where the turtleback started it's ease to the hull.
Like I said earlier...sorry that my memory didn't help you in exact measurements.