Ok, most of these aren't KM specific.
The Abort Mission button crashing the game (that's actually what happens) is known to happen on some large installs (scripts-wise). I suspect it's because of unreleased resources, but since we don't know what is causing it, we can't resolve it.
Abandon Ship issue, have you tried alt+tabbing out of BC, and checked if there is a window with the BC logo/icon?
If there is, that's a console, take a screenshot of it and post it here. This isn't a KM problem, that debug console can pop-up on some errors it thinks are rather important. It also causes BC to "freeze" (pause is a way better word in this case).
Some systems aren't actually meant to be played, though I think these are.
Go through the readme and find the original authors and ask them.
The source folder doesn't go anywhere unless you want to know the source, the installation instructions don't mention them, and only scripters would have an use for them.