It's late, so I apologize for anything that sounds crazy or anything I missed. Here's my comments, super bulleted list style. It's a good project you're working on, so please don't take any of my notes as being in any way mean spirited.
Battleships/Carriers Document
* CSS v. TCS. 'CSS' is only seen in the original game (the CSS Suffolk) and on the movie patches. In the latter case, 'TCS' is used in spoken dialogue in the movie. The idea that they go from 'CSS' to 'TCS' at some point doesn't make sense because we see ships with the latter earlier and the former later. It's such a tiny reference, too, that it's probably not necessary going through all this to try and explain it. (Easier explanation: the Suffolk belongs to some other Alliance faction.)
* Cruise Missiles. You give a lot of ship classes cruise missiles... but to the best of my knowledge, they don't actually show up anywhere in Wing Commander.
* 'Bathesda' should be 'Bethesda'.
* 'Solus Planum' should be 'Solis Planum'.
* 'Perron' should be 'Peron'.
* The reference to selling a battleship to the Goddard militia is awkward, because it doesn't really make sense. For one thing, a militia buying a battleship sounds more like the punch line to the joke about the Air Force having a bake sale than it does something that could actually happen. Can you see the USN ever selling an Iowa-class battleship to anyone as anything but scrap (similarly, can you ever see the Coast Guard or a private militia unit operating a ship like that?). Second, a battleship to defend Goddard would change the story of The Secret Missions -- why rush to Goddard when they've got a
battleship to protect them!
* You gave the 2537-vintage battleship torpedoes.
* There's a reason armor is given in equivalents everywhere -- because doing multipliers in your head makes comparing values awkward. Just give everything in durasteel equivalents.
* The TCS North Carolina survied McAuliffe.
* One of the weapons mentioned in Action Stations is mine launchers onboard the North Carolina.
* Ranger-class needs a CapShip Missile Launcher - and as long as you're handing out weapons, throw these onto some of the 'older' ships, per Victory Streak.
* Action Stations implies that pre-war fleets are built around ten battleships and three carriers. Two such fleets participate in the Panama System War Games (2622)... which is to say, you need more ships.
* Your crew complements in general seem high -- but specifically the Bengal-class. The complement given with the "Flight I" specifications in TCH is 600, and the complement given for the Tiger's Claw in the WC12USG is 750.
* The Bengal-class is already far too heavily armed. Don't give it missile launchers.
* No need to create a system of variants for the Anti-Matter Guns -- all the guns in Wing Commander increase in capacity throughout the timeline.
* There's a reference to the Concordia-class having 84 fighters circa Action Stations. You could work that in.
* 150 kps for the Concordia-class Fleet Carrier.
* Based on an End Run reference, I'd give the Jutland-class 167 fighters and 3,400 crew.
* 2660 is the earliest date for the Confederation-class, as we need five years from the capture of the Sivar's remains (2655) to build the first one.
* Don't add lasers to the Confederation-class.
* I'm not a fan of adding 'Island' after 'Wake' for the CVEs.
* Service entry date for the CVEs is 2667.
* Fighter complement for the CVEs is 45 (three squadrons of 15).
* The history note is wrong, the CVEs were nine (military) heavy transports converted into escort carriers.
* The speeds given in End Run for the Tarawa are 100 kps cruising, 247 kps maximum and 10,080 kps scoops closed.
* Weapons included one quad-barelled heavy neutron cannon, two medium caliber mass driver cannons, two particle cannons and several missile launch racks (single tube).
* Lexington-class is a Heavy Carrier, length should be 725 meters. Mass is the ever-disappointing 3,250 tonnes. Speed is 50 kps. Weapons should be ten flak guns.
* 60 seems like an awful lot of fighters for an escort carrier (Eagle). I've also never liked the idea of calling the darned things Eagle-class just because we happen to see one named Eagle.
* Crew complement for the Vesuvius-class should be 7,800.
* Your Behemoth-class specs are very odd. First, I'd drop the old fan-made 'dreadnaught' classification and refer to it as a Behemoth-class Weapons Platform (re: the WC3 PSX guide). Then I'd throw out all the heavy weapons and fighters you're giving it because... it's the Behemoth, it's not a carrier, it's a giant space gun, not an ordinary ship of the line.
* The Midway entered service in 2680.
* All of the Midway's laser-turrets were dual mount, and she also had six IFF missile launchers.
Cruisers/Destroyers Document
* First off, production runs. Destroyers and cruisers should make up the bulk of both fleets -- TCH claims the Kilrathi have thousands of Ralari and Fralthi... presumably, the Confederation has similar numbers for its tin cans, and that a lot of the war we don't see in our carrier games is destroyer and cruiser base battles.
* Kudos on Antietam as a theoretical class name... though I have half a mind to suggest you go with the strange example of the TCS Manassas and call it Sharpsburg-class

* Crew complement for the Tallahassee-class is 360.
* The WC3 'frigate' is a destroyer model, not a cruiser model. The frigate thing is odd, I'm not sure what you're trying to explain.
* Crew complement of the Concordia-class is 700. Fighter complement is twenty.
* Gettysburg class is a plain Cruiser, no 'Heavy' (Fleet Tactics at work).
* You forgot my favorite Concordia-class ship, the TCS McClellan.
* The Gettysburg-class carrier a single squadron of fighters (16?).
* I'm not going to fool with the Plunkett or Murphy, save to suggest you look at
https://www.wcnews.com/loaf/Murphy.doc and
https://www.wcnews.com/loaf/Plunkett.doc
* The Union of Border Worlds didn't exist in 2672.
* Can somebody find the actual passage about the Valiant-class? Because I can't find it.
* The TPoF novelization claims that Caernavon-class ships are being retired after the war -- so they won't be around in 2682.