It's hard to see where the two regimes are separated, really.
Pakistan was the first country to recognize the Taliban is afghanistan's defacto power base in 1997. Mussaref has yet to arrest a single major taliban player. The particular brand of islam practiced by the taliban is widely observed within pakistan and (unconfirmed) rumours have it that the taliban + pakistan have colluded to engage in small-scale insurgencies on India over the disputed Kasmir region.
I wouldn't go so far as to say that the taliban and the current regime in pakistan are one and the same, but there's obvious close ties and mutual admiration, and no evidence that those ties have weakened in the last 3 years.
That said, it should be pointed out that the Taliban itself has not been proven to engage in state sponsored terrorism (that I'm aware of) aside from that of giving aid and comfort to islamic extremeists. The 2002 invasion of Afghanistan was not because 'afghanistan attacked someone', it was because they provided training area and (presumably) material support to Al Qaeda and other radical islamist groups. All the actors on 9/11 were majority Saudi, with some UAE, Lebanese and one Egyptian (atta)... not one hailed from afghanistan. However, afghanistan, being a non-oil-producing arab nation with an extremist regime that most people wanted to see gone anyways, was a much more suitable target for bloodlust and retaliation than the saudi easily-disrupted oil fields that would send prices sky high in a heartbeat, torqueing the world into an economic collapse.
It's ironic that afghanistan, being so used to war, basically treated the invasion as yet another incursion in a long list and adapted accordingly... The once-scatted taliban is re-coalescing and on the ascendant, and everywhere outside of kandahar has once again reverted to the playgrounds of the warlords. Sum total accomplishment: put the country back to the state just prior to the taliban's rise (early to mid 90s era).
FWIW, the Taliban have never been any sort of real concern aside from being an 'aligned interest'. If you want to be paranoid about suitcase nukes hitting the fatherland, cast a wary eye at old soviet technology which goes missing at an alarming rate. Some of those guys would sell their mother's kidneys for a case of Stolichnaya, with their mother still attached.
