Okay. I have uploaded Mantle 1.0.2. Give it a try if you get the chance.
I finally went and looked at the campaign file, and my HoL weapon variants weren't tagged as available at the start, so it's possible this all just happened because I'm a derp. So, I fixed that.
I'm not convinced that was the problem, or the whole problem, though; I'm almost positive that I tested the campaign using the ready room itself, not just the tech room, and that the loadouts were fine. I also think that I went through and made sure the campaign file was correct before releasing 1.0.0, though I could be wrong... So, maybe it reset itself or something?
Anyway. Let me know if the loadout nonsense is still happening in this version. The other problems may take longer to fix -- for that matter, the instability in the last two missions might be unavoidable (assuming I want to keep them basically as-is in terms of gameplay). I think there might just be too much stuff happening in those missions for the engine to reliably handle.