Most people who have done any of these trophies have said they had to do the missions in order so that the save file you use to beat the game has all the missions completed with no kills and no alerts contained within it. So if you get to a mission stat screen and see that you messed up, you have to reload an earlier save file and redo the mission immediately. When you replay those missions out of order you are essentially starting a new save file that doesn't have a record of all your missions.
So play with at least two save files. Get perfect stats on one for mission 1. Then start saving on a second save file and do not save over the first save file. If you complete mission 2 perfectly you can save over save file 1 and leave save file 2. If you messed up, reload save file 1 and start mission 2 over again, but keep your original save file 1 intact and only save on top of save file 2 in case you mess up again. Eventually you need a single save file with all mission played perfect in order. That is how I got shadow.
Now as for ghost and clean hands there are other glitches/hidden requirments that haven't been solved completely. The ones we know about have been posted elsewhere by the forum administrator:
How do I meet the requirements for the ‘Ghost/Shadow/Specter/Faceless/Clean Hands’ Achievements/Trophies?