I think that Aghanistan was a threat to national security. I think that Iraq was a threat to national security. I think that had the Afghanistan govt had the brains to work with the US, we wouldn't have invaded the country and overthrown the regime. I think that if Saddam had fully cooperated with UN inspectors we wouldn't have invaded that country.
I think these countries would stop being a threat IF they took steps towards cooperation.
I don't think of Pakistan as a threat because it is taken some steps towards cooperation. I see Pakistan as taking extraordinary steps in cooperation [but I see them they taking advantage of your strong interest in working with them- therefore the extrardinary degree is more of their choice rather what we are asking for]. Pakistan remain a general threat because it is fairly unstable and because it has "problems" with India. And because both Pakistan and India have nuclear weapons there is still a possiblity of Pakistan being a national security problem for us. BUT at the moment they apparently going in the right direction. So it makes sense to try to build a relationship which evenually will lead to a situation in which they are no longer as potentially threatening.

As far as dirty bombs- I agree that they are not threat IF people are rational. But we aren't rational. Small unlikely risks commonly terrorize people. In a sense a dirty bomb exploding in a major city US could long term benefit- people might become less terrified of anything "nuclear"- but short term the "damage" would be major.
Rationally, the war in Iraq and Afghanistan is basically over. The current problem is perception. For example, Kosovo currently is just as unresolved as Iraq. Kosovo is small country, we are bored with it, it wasn't that important, and whatever. Iraq on the other hand is in the middle of everything. But even Iraq after our election will probably become less important- at least as far as US public is concerned. I expect it will become more important to Europeans- because Iraq is actually important and it will affect countries in the region- which includes Europe.
Look at India- very important country, and lots of problems and conflicts- and it never gets much attention from US public.
Probably after the elections the US public will return most of it attention to domestic stuff. Unless something else in the world demands our attention- Sudan is possible but not likely.