A bit more of a rundown: You read Stony Man? Somewhat similar, except that it's closer to a company in size(I get that right? A few hundred fighters in the unit), and they have had a considerable budget since the beginning of the Cold War, when the unit was formed based on past temporary units in other wars, to do ultra-covert stuff in other countries, and sometimes in this one. Their existance was recently declassified to allow them to take on other duties.
The thing with the callsigns is that each member has a permanent callsign, which is used instead of a name. Thier real names are classified, not even their commander knows everything, allowing them to be sheltered from the political process, allowing them to do their job without alot of stuff that cops and the army have to worry about(without this you might as well use the army). I can see temporary callsigns in combat, but when the news, or Congress, or anyone else refers to one, they use the callsign. Among the members of a team, you might use a nickname, or something, but even they don't know who you are when you aren't blowing stuff up(one drawback to using the unit is alot of collatoral damage, they do whatever's needed to achieve the objective). The method I was thinking of was this: A letter to indicate a security status(how bad of a compromise is it if someone finds out who you are; if you think about it, they have alot of enemies, not all of them nice), a number to distinguish individuality, and the team names are colors. For example, the main character is leader of Blue Team, his sign is B12, The Bravo being because he's so nasty in combat no one would willingly mess with him, even indirectly, and then the twelve to destinguish him from all the other people with Bravo classification. Does that work? There are armored units, and air cover, I figured I'd play a conspiracy theory and make their trademark vehicles black, unmarked. A few Apaches in there...
Here's the forum if you're interested, Sniper, Apparently she hasn't gotten back to me yet, perhaps if you put in a good word...
http://angelsofiron.conforums.com/index.cgi
"Some pup"
Nickname by Fenderstrat72