/suggestions:
Chap 1 <-> 3
~Mark Soban's Arrow Scout.
As he flew around with it (and later in a Blade Interceptor), I recall you involving buttons similar to the controls of the HW1 game; Passive, Aggressive, Neutral.
To me, this is a bit too close to the game. While I am sure that there would be such, I would find it better if you were to give these three specific tactical names and/or have Mark notice/explain the changes to his fighter's maneuverability.
My mind is not clear on physics of HW1 but I think you do more dmg in the game when on Aggressive stance; however, I find it hard to reconsider this here as the weaponry is more likely "Projectile" than heat/energetic based. Personally, I'd say you should invent something like what was in HWC with the Acolyte fighter. Setting Aggressive would cause the fighter to expose nodes, cannons or anything that would cause it to be more vulnerable to enemy fire or micro space debris. Okay, that is probably going too far, but that is just a lousy suggestion

.
Same could go however for passive/defensive stance; the fighter would engage a lot more to its vernier/maneuvering thrusters as well as have a computer to engage lightning fast positional changes without distracting the pilot's aim much. This would burn more fuel or such.
~ The atmo testflight.
You mentioned something about a loose screw, however how did the character know about it?
I don't want to be picky ;D. I'd say it would be better to have a series of malfunctions cascade to him having to get to a lower orbit in order not to burn until he'd reach atmosphere service again. Or perhaps make him figure that out by learning that one of the mechanics had screwed up (no word pun intended, for a change) after investigations. You could add that Mark was charged at first and nearly got releaved from duty.
~ Add more stress.
Just a minor one, add more stress like inertia and the pain of moving back and forth in a cockpit. I'm certain that at that time of the Kharakian Genocide, nothing was that comfortable (although you stated most of it well enough). Just when in combat, he should be feeling the physics.
/nitpicks
I'm not one who is good with the time tenses but there are several occassions where the time tenses get a bit confusing due to a moment of bouncing between past and present tenses. I tend to do this too, but whenever I am forced to use one or the other, I'd suggest to write a whole paragraph in that tense for a while and put in all that needs to be "happnening or seen at that moment". At the moment (and if I remember correctly) there were things that had happened, but got tied with the 1st person speech of Mark.
~Turanic Raiders.
As fleet intelligence figured who the first foes were, I found it that the story about them such as liquid-oxygen etc was revealed too early - especially for the fact that Mark was still in space. However, since this is more of a live story-telling, I may be seeing things wrong and Mark just noted the remark of who these people were.
On the other hand, maybe it would be better to have the Mothership fleet capture one of the turanics as well as later the taiidans. Later on when the Mothership leaves Kharakian space for good, Mark would hear the tales of fellow crewmen on the Turanics; how they look like, what they wore etc.
I liked the idea of the grilled Kharak being a scorched-glass marble. I always thought it to be nothing more but a barren dust ball ever since. I don't know if it was said to be glass in the game, but if not, great idea. I'd almost dare to incorporate it in my stories if I should ever do something regarding post-Kharak.
Okay I don't want to melt you down with too much blathering of mine

. Cya soon(tm)