That sounds like you installed TBP to the Knossos app directory, which, for future reference, you should definitely not do. The FSO and the FS data files should be completely separate from where the Knossos app is installed. Right now, your installation is so bad the easiest way of fixing it might be completely removing and reinstalling everything like you said.
Achen should be left as a campaign since it's currently the default campaign, which is desirable for people who are first playing Freespace. We can change the default training campaign to Io but I don't see a good reason to make Achen into a techroom mission only.
Personally, I'd rather not start including more campaigns in the initial release, since that's just more for us to test. Pretty much all major projects have multiple testers, so before we release I'd like to run through it myself (I'm playing a mission a day and I have a bunch of free time coming up, so I can step it up soon).
I'll fix the detail level warning today.
Also I seem to remember a warning about missing weapons in the atmospheric mission that I'm not sure has been fixed, so I'll look into that when I get there.