As creator of the campaign I can asure you two things:
a) There is no such things as a deliberate order to scan the fighters in that mission ...
technically there should be no problem; the event only checks if all 15 fighters have been scanned... (in earlier versions there was a bug that prevented one fighter from becoming visible so it could not be scanned)
b) You can always skip scanning the fighters ... the mission will continue once you've scanned any subsystem on the C'Tan
The final mission is ... the final mission and as such a tad more difficult than the rest ... however what you tell me makes me things somthing has broken it along the way... I'll check it and add it to the updates list...
The worst case scenario is the station dies too late so your Narn cruiser will be much too close to it and then be killed in seconds.
Is it killed by enemy fire or by the debris shower from the station? - the Debris shower is a problem that cannot be fixed by FREDing...
The first EA ship appears and is destroyed like it's probably intended.
It is intended
Of course the latter never ever uses its powerbeams while the Drakh cruisers use them all the time.
Acutally I should be beam-freed - but maybe I forgot to guardian those turrets ... are you sure the drakh fighters didn't kill those turrets outright?
I can't even figure out how to increase the ships hulls in the fs2 file [...] I suspect it has something to do with the "campaign-persistent" variables, but what should I use instead?
For realisms sake I used "campaign persistent" variables to transfer the hull-value in percent from one mission to the other... they are transfered onto a ship with the same name in the next mission only with a slight increase in some missions
As I said before... days have only 24 houres each and I can't fit everything into those I wish I could (otherwise I would have checked, fixed and uploaded an update LONG ago)...
BTW, what are the projects you are working on right now? More cool The Babylon Project stuff or something else?
I've been interviewed (http://www.hard-light.net/forums/index.php?topic=69173.0) on that subject by Stormkeeper more than a year ago... (although since then I've wrote one more TBP campaign outline I won't turn into working missions 'cause I will not have to time)