Disclaimer: I never played the original mod, so I can't say I have a "feel" for what the faction should have/did play like compared to vanilla balance back in the day. I'm just giving it my best go at it compared to how it plays with the game right now.
The vast majority of ballistics will need a substantial balance pass once their ammo restriction is removed -- right now most of (all?) the kinetic weapons all put out higher DPS than their flux cost, for example, which is not the norm for most vanilla weapons outside of some small mounts and the needlers. For example, the Mass Driver has the same range, accuracy, traverse etc as the Hypervelocity Driver -- but it does 208 DPS for 167 flux/s, while the HD does 138 DPS for 178 flux/s, *and* the Mass Driver has exceptional armor penetration with its 1,500 damage shot. This is all worth far more than 17 OP. Another big offender is the Cain, which beats out the Mjolnir in efficiency and the plasma cannon for raw energy damage. For starters, I'd suggest going through the medium/large ballistic weapons and inverting their DPS and flux/s where appropriate... that seems like it might be a good starting point.
Some of the missiles will need to be reworked too. Right now the medium MLRS mount is pretty much a strictly inferior Annihilator -- 800 vs. 1500 range is a cripplingly bad deficit, and it has few other features that justify a 50% OP cost increase. The large mount at least does substantially more damage, but the range is still incredibly restrictive. Even SRMs reach 1,000.
Like Surge mentioned, the fighters need a substantial balance pass as well. Both the Tracer and the Hornet are very slow at 100 and 125, barely capable of catching capitals with the zero-flux boost on, making them incredibly vulnerable to defensive fire... especially the Tracer, since it closes to a pretty short range to drop its torpedoes compared to the Atropos-equipped vanilla bombers. Even the Warthog goes 130, and the Piranha 150. The Foxbat has an acceptable speed of 200, but even that is only comparable to heavy fighters, and far lower than most other fighters classified as "interceptors," a number of which exceed 300.
Also, I believe the Hornet should get the *single* Sabot launchers like the Longbow uses. It's not necessarily imbalanced if it has 2 Sabots instead of the 1 the Longbow has, but right now it's using a pair of the standard Small Missile Mount Sabots, not the Longbow's single-shot fighter version, which makes it ludicrously overpowered as a single 8-OP wing of them is dumping 12 Sabots in a pass! With higher speeds, they'll also need higher OP costs; the Tracer is only 12 OP compared to the 20/28 for the Dagger/Trident; and the Tracer is 4 less than the Longbow, which has half the Sabots.
The Antares and Zephyr are still using point-defense drones as their ship systems; and the Mercury has sensor drones. The standard now is to have drones as a built-in fighter bay, with something else as a ship system, so that's something to consider an alternative for. Also, the Antares just sucks in general: too few weapons mounts, flux stats no better than a cruiser, *and* slower than either of the vanilla battlecruisers... despite a 40-supply deployment cost like the Conquest.
I can't really comment on the balance of anything but the capitals, as they're all I've experimented with in the simulator so far. As mentioned, the Antares sucks. The Auria and Titan feel like they're in a pretty good place, and the Yukon feels balanced for its deployment cost -- but its stats are more those of a cruiser than a capital, so it might stand to be reclassified. EDIT: the Titan might be a bit *too* good actually; the teleporter is incredibly powerful. Perhaps should get a higher flux cost, or fewer uses/longer recharge. /EDIT
More minor quibbles, but worth noting: missing ship, ship system, and item descriptions all over the place. Various typos in some others ("Hedgemony" instead of "Hegemony" in the Antares description, for example). Lack of Autofit options for the ships. CR costs on deployment are very low (about 1/2 vanilla numbers) across the board -- not sure if that was an intentional balance point for the mod, or just a different standard for an older version of the game.
Hope that helps!