These were covered a long time ago by someoneelse. Threfore, what I write here is from memory. I have it somewhere but I'll need time to find it (if someone has it, fell free).
CIA sited mostly with civgog and I like the cannon idea of having DIA taking over.
FBI was stated as being kind of neutral and operating in both civgov and milgov. Nevertheless, it had its central office in Denver and more agent were operating in milgov areas.
DEA I have no real clue. However, I would expect its members and euipments to site with whomever is in charge. Whatever, the agency would be disolved and its agents would have switch mission. I don't expect anyone to care any more about drug traffics except in order to use drugs as weapon of war. We often forget it (and keep it silent today) but drugs were all developped (as they exist today) by western militaries to weaken asian powers. The British favored opium in China, the French used drugs in their conquest of Indochina... Saddly our weapons have been turned against us.
About counter terrorist units, I think that they would continue to exist where they exist, being used in very specific situations. Anyway, these highly specialized groups are very limited in number. IMO they would be uused for highly sensitive special ops.
Then, General, you forgot about two things. I think that Scotland Yard would still be around (even at an international level) while I would count that interpol would maintain some operations. To my surprise I discovered that it was created in 1923. Located in Lyon, it would certainly have survived the war (Lyon was spared) and at least 3 of its international offices could survive (Salvador, Kenya and Thailand). In addition at the time of T2K it was headed by a british. However, it remains only a kind of survey tool and will take little action (if any). By the way I'll be interested in finding about its status during WW2. It had been headed by an Austrian (Oskar Dressler) from 1932 to 1946.