I'd guess that any super-black side SOF unit doing CT missions would recruit heavily from, and consequently emulate, the super cool kids in JSOC.
Depending on the size of the organization you're thinking about, it sounds like you might be looking at something like:
1) Assault element -- maybe based on four man assault teams, and probably the least compartmentalized, as for any target requiring multiple teams you'd have to have guys training together. If the overall organization is large enough maybe they compartmentalize at a 12 or 16 man troop or platoon (or some non-CAG/SEAL term).
2) Targeting element -- The HUMINT side of intel and RSTA, or maybe both human assets and the more technical guys both fall under this. Develop targets for the Assault guys, and/or cruise missiles/JDAMs/etc. Probably work in smaller groups, and possibly equipped to take direct action against a sufficiently time sensitive HVT if need be.
3) Technical Resources element -- The guys on loan from the NSA or whatever who do SIGINT, point all of the ECHELON system at one single bad guy's cell phone and email accounts, etc.
4) Support element -- The supply (including cool Q Workshop type stuff) guys, dedicated medical and commo assets, and whatever administrative/enabling slice the organization needs. (Again, whether this is a couple guys who wear 20 different hats apiece or a room full of bureaucrats depends on how large you envision the organization being.)
Is the organization big enough that you see them owning their own big ticket items like black helicopters, C-17s, and small/fast naval assets, etc., or would that stuff be borrowed/commandeered from other agencies if/when needed? If there's major equipment like that under the same umbrella, the support element might be significantly more elaborate.
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