If you want to train bravery for a specific gal, just set her to nude for a mission or two. As long as the mission isn't really short, the extra combat stress will eventually panic her, which she'll recover from, and train the stat. Even +20 bravery is worth it from a couple of missions, more stats if she actually does a bit of stuff. Hazing rookies is great.
It's a pretty good idea to not give her pre-primed grenades or anything though, in case deaths berserk her. If she just sits in the Bonny and throws down necessary items, she'll still panic eventually, but she's doing something kind of useful. Then again, great stamina kind of begs to be given a mêlée/energy using weapon of some sort. And does stats even better after a few swings.
I'll have to try out the flags more often. I never use them, but they might fit great with my style of play.