I'm writing a story that could end up with a battle between a squadron of alien invaders and a present-day U.S. Navy carrier battle group, and I'd like to insert some appropriate chunks of jargon in scenes aboard the ships. I can find dictionaries of individual words, but are there any references containing appropriate strings of text that would occur? Ideally I'd like something with the flavor of http://the-alt-historian.tumblr.com/post/98308097485/we-have-some-transmissions-from-the-persian except more realistic.
As I understand you are looking for some reference on US type naval warfare. The Las Ship tv series would be the perfect reference, as it's a story about the last US Destroyer, so they have only minimum resources and only have to use strategic tactics when coming across different challenges. I have watched all the season of this series and I can tell you that it contains strategy about fighting water to air, water to land and water to water combats. Especially in situations when they had to fight a Soviet Submarine and a Soviet Destroyer.
A Few simple things in addition to the slang terms you have to make your dialogue more Navy-ish:
Military Time: Time references should use a 24 hour clock. I.E. nothing ever happens at 2:30 (two thirty) it would be 1430 (fourteen thirty).
Nautical Reference Directions: Onboard ship, directions are based on the ship, instead of right, left, North South, etc. you have port/starboard and forward/aft.
Acronyms: In the military they have a lot of long winded names for everything, which always get abbreviated to an acronym when used by actual sailors. Throw some relevant ones into the mix. https://en.wikipedia.org/wiki/List_of_U.S._Navy_acronyms
Phonetic Alphabet: In combination with the use of acronyms, the phonetic alphabet is also often used. For example you might regularly hear someone say "Whisky Tango Foxtrot" for WTF (What the Fuck?) which brings up the next point.
Expletives: "Curse like a Sailor" is a phrase that exists for a reason, expect some salty language in your dialogue.
In general you should figure out what dialogue your story needs to tell the story and maybe spice it up to give it some light Navy flavor, too much naval slang will either be unrecognizable to regular readers (or require excessive explanation which is a story killer), or you'll get it wrong offending any readers with Navy experience. If you cannot figure out what the slang means to string together coherent sentences, don't expect your readers to understand it, and leave it out.