Apologies for the late response.
Maybe I'm just really bad at stealth missions, but I swear, every time I've failed that one where you're supposed to target all the Shivan ships, there hasn't been anything anywhere near the three hundred meter cutoff on the proximity gauge. What's going on here?
The proximity gauge only indicates fighters, but the sentry guns will detect you as well.
This is intentional, but maybe I should change it. (Originally, there was no proximity gauge, and it was added in order to help you track the things that moved around, while relying on the player to track things that were stationary.)
Okay, maybe I just suck,, but I am finding the mission "perfect vision" where I have to guard the two ships while they are scanning the system in the GTVA branch to be literally impossible, even on very easy difficulty I failed 4 times in a row so far. They are so easy to kill it's simply impossible to prevent the far too many shivan fighters from doing so. And I am ignoring the convoy completely, I stay near the ships all the time,a nd kill about one fighter every 5 seconds, making sure to target the ones attacking either of the ships and that time and ordering my wingmates to do the same. Despite all this, I just failed for the fourth time on very easy.
What am I doing wrong? I want to get to the next mission 
EDIT: never mind, made it the fifth time on very easy... but you might want to make it a bit easier! 
This mission somehow got quite a bit harder since it was first FREDded. I can only assume SCP changes are to blame, but I'm not sure exactly what causes it. That's why I made engaging the convoy a secondary objective - originally, it was required.
Did you try it on Medium difficulty? Friendly fighters are more intelligent on Medium.
Great campaign overall!
Thanks!
Allright now I am in the mission where I have to protect the US- I mean GTD Enterprise from the kraken, and I get the message that the kraken has only one beam turret and I should fire 4 trebuchet missiles at it. I target a beam turret on the kraken, destroy it with said 4 missiles, but turns out it had more then one operational after all and it destroys the Enterprise and I fail the mission. Is that supposed to happen? :-/
Also, I already lost the arnku before that, but given that the mission goes on like nothing happened I assume that will not result in a mission failed debriefing right?
That would be one
primary beam turret, on the forward prongs of the Kraken. There are other beam turrets operational, but they are anti-fighter turrets and not a threat to the Enterprise.
It is possible to save the Arnku, but very difficult. The story assumes that the Arnku will be lost.