I would argue 1 and 2 are AQ and its UW network. We should quietly, ruthlessly and persistently capture/kill 1 and disrupt 2.
How do you reconcile that with this:

Actually my primary concern with Pakistan has very little to do with AQ or the Taliban and has everything to do with how our pursuit of both is changing the delicate balance of deterrence between Pakistan and India.
...considering that most of those in category 1 and many in 2 are in those "ungoverned" Pakistani spaces? If not drone strikes, then what? The drone strikes are extremely unpopular among the domestic Pakistani population and I think they are having a destabilizing effect on Pakistan itself. Is there something else that can kill/capture 1 and disrupt 2 in without all the negative effects of drone strikes?

This article is actually pretty good in how it lays out the fact that AQ is a larger problem today than they were 9 years ago
That's a common assertion - one that I think is supported by little evidence.