1) No, there is no better manual, or at least I haven't been able to find one.
2)The only windows-based software Zeiss uses is Calypso, which is a new NT-based high-end solution. It's considerably beyond the C400 level.
3)You should be able to measure any shape which can be described in GD&T, as long as your probes can physically touch the surfaces. However, extracting useful information from it can be an exercise in ingenuity!

My best advice is to make a conscious effort to use 3-D features all the time; that way you can easily change the interrelations of features on your fins.