Here is my debug log, I think.
The next one I'll be playing is Twilight (I just hope it doesn't involve any sparkling vampires).
Also since I was playing these from the tech room I couldn't see the new medal, and I also just realized there is an option in the campaign room to start the campaign again from the branch point, but it's too late for that now.
You can choose the directory where the mods are installed. In fact, people really shouldn't use C:\Program Files for that since it complicates a few things. Please note that this directory is separate from the location where Knossos is installed. You can select both, one during installation and the other on first run. You should also use a new directory since Knossos has a different directory structure. It will copy the retail VPs from your old directory if you point Knossos towards it when it asks you to.
Regarding the bold text above, you mean the Knossos "data path" under Settings should be separate from my existing installation, right?
So I have the the Knossos folder (E:\Program Files (x86)\Knossos), my existing folder (E:\games\FreeSpace2), and I will create a new folder for Knossos downloads?
Correct - the knossos downloads dir could be something like E:\games\FS2Knossos
Mission 6 (Military Branch): I knew I was going to hate this mission as soon as I read the briefing. Escorting warheads by firing EMP missiles sounded impossible, and indeed that was my experience in the mission. Nothing I did could stop the missiles from being shot down, it was pure luck that any of them survived, and even when they did they did hardly any damage to the turret. I failed the mission tons of times and eventually had to cheat and destroy the turrets with cheat codes. Even when I did that, though, there was an error when the AWACs ship showed up, Delta wing arrived shortly before I destroyed the ship and the mission ended successfully (as I cheated again to destroy the last turret) but the debriefing gave both the successful text and text saying that one turret wasn't destroyed and I didn't signal Delta wing. I have no idea what was going on there.