To avoid confusion, you might wanna consider giving your campaign a different name before release. TopAce released a post-Capella campaign just a couple years back called Luyten Civil War (http://www.hard-light.net/forums/index.php?topic=81110.0), so a title that makes yours stand out a bit more might be a good call.
"In 2358, 5 years after the end of the Second Shivan Incursion, the economic downturn still rampaged the distant GTVA worlds, on which too much pressure was put on the building Delta-Serpentis Jump gate, border systems like Adhara or Laramis faces a economic collapse and poverty to its citizens, plagues spread and small militias raised in revocation of BETAC of said systems. From now on, they are called independent.
With GTVA still too much occupied in its core systems and Jump gate building project there were never been able to accordingly respond to those uprisings, any real funding on still loyal border worlds was non-existent, and they which found themselves alone in the midst of their new problems, Adharian Confederacy and Laramis Supreme Reign.
GTVA still underestimated there civil unrest, believing that those will collapse themselves, diplomatic ties has been established only 6 months later, after the official forming of those new system-states.
Failed diplomacy and still neglected border systems of GTVA faced a total economic breakdown and anarchy, they could not sustain itself without outer help, help which GTVA still didn't handed.
After 4 months, those who finally realized that GTVA won't help them any way, they turned their looks on the two minor factions, the Adhara and Laramis, which economic state was growing up after secession from GTVA, in one year, many of border systems joined first or second faction, forming two formidable powers to be reckoned with, in time, they formed a strong military presence to backbone their independence ambitions.
GTVA could not ignore that, again, next 2 months of failed diplomacy sparkled a conflict between Laramis Supreme Reign and GTVA, still devastated military of the Alliance Terran part could not hold its territories, until Vasudan Armada finally joined the fight in 2351, beating the Supreme Reign and driving their fleet back to their home system.
This could become a start to and end of the Laramis uprising, if not Adharians, still untouched by any conflict, came to aid the Laramis people, after a bloody war that endured for 4 years, the new forged allies, were able to stop GTVA advance.
Both parties understood that they can't hold their independence by their very own, 2 years later, in 2357, they formed a one, and unified front to fight with the still hostile GTVA, any contact has been cut down, and new war started."
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"At the end of 2357, culminating the end of the most bloody civil war known, Adharian Confederacy and Laramis Supreme Reign faced a problem, while their military crippled and beaten, a still hostile GTVA endured. Most likely that in next year, the existence of said factions would come to and violent end at the tip of Alliance's gunpoint's. The leaders of said minor powers in border worlds met in Wolf system, signing a truce, an pact that brought a new, independent and strong faction to power, the 'Wolf's Allied Convention' formed Star Alliance, which officially came to life in 2359, when a capital was chosen in Adhara system. The known two faction became one, with a strong anti-alliance propaganda they managed to rally everyone on their controlled territories. A new, unified front evolve to ensure safety from GTVA. For the next 10 years, the Alliance was uncontested by GTVA, diplomatic channels were opened as of 2362 and a cease-fire was enacted. The back down economy was finally to recover on the much suffered border worlds."Okay, this version is beatable. Your FREDding has certainly improved; if you remember what you've learned here, you should be able to make solid missions. Nice touch, tying in the Vaspado's beam shot to the capture and availability of Capella-era ships in future missions (can I have Kaysers and Tornados plz ;))
Weakening subsystems by setting their strength to lower percentages looks odd in-mission (like those subsystems were damaged, even on fresh ships.) The best way to weaken or strengthen individual ship subsystems is by using armor types provided in your mod's Armor.tbl, though table-editing goes beyond the scope of mere FREDding.
Taking out the Naeros's subsystems is still a bit tedious (especially if you've lost all your wingmen already.) Maybe have a wing of allied bombers with Stiletto IIs jump in to disable the station's subsystems, and you have to defend the bombers from one last wave of enemy fighters while they do their job?
BTW, why is the player flying for the anti-GTVA rebel faction?
actually, your story seems to show compatibilities with the end telling of the luyten civil war, as such, would you not be tempted to try and link both in one continuity, like STR and echo gate?