Yes, your builds seemed to have fixed it when I was trying capship missions.
Obvously, I can't use support craft. I will make it so when you push a key, all your weapons will stop firing for about 30 seconds. After this period, you will gain 15% more health to all your non-weapon subsystems. Another key will make you stop firing for 45 seconds, and afterwards will give you 30% more health to your weapon subsystems. This is supposed to make your ship operational, not set to full capacity. If your engines are killed or your beams are blown up, its going to sacrifice you at least 30 seconds, but not the whole mission.
The first mission will involve you as a Hipocrates. The mission objectives are to survive to the jump node and (as the only ship with an anti-cap beam) ensure the safety of the other ships in the case of attack. You will be between a Zephyrus and a couple Argos at the start of the mission, with a wing of Myrmidons guarding each ship (the Argos count as one). Alpha wing is assigned to you, and you have control over it and no others. Soon your group will be attacked from the left, putting the Argos in danger. The enemies include two wings of Hercules and a Fenris, all of which have just been sent into service. The Argos will have an AI order to go above you and the Zephyrus to be on the right of the group, but the enemy should be able to destroy them before they get there, provided that you do not intervene. If an argo is destroyed, command will tell you not to let the other die. If both are killed, command will yell at you and relieve you of your command, and the mission will end. If you succeed against the two Hercules wings, the Fenris will start firing its beams, so a kill of its turret before it decides to fire is a good idea. If for some bizarre reason the Fenris is destroyed before the fighters are, the fighters will kamakaze against... you guessed it, YOU! They don't do all that much damage, but they are going for your engines, so be careful with the fighters. The second wave includes a battered leviathan which has 50% health and the subsystems are randomly damaged from 25% to 100%, and on top of all that, it lost its main beam cannon! However, it has two more wings of Hercules coming your way. Because they are coming from the front, you should have no problem attacking the Leviathan (which is turned to that it is facing you from the side). The fighters, however, will be a problem. Luckily, they are not interested in you... they are interested in the Zephyrus, and if you lose the Zephyrus, not only will you fail the mission if you already lost an Argo, you will also risk losing both you and the Argos to the large gas explosion. When the Leviathan is knocked to 10%, it will self destruct, and the fighters will jump out. By now, you should be almost to the Jump node, which is the good news. The bad news is that a Medusa wing is coming from behind you! If you didn't stop for repairs, you should be able to avoid a confrontation. The next mission will either be another Hipocrates mission, or you will be promoted to the captain of the Fenris, GTC Vertigo. The first mission is all about being in the right place at the right time, but all first missions are easy, arent they?