I voted, not with full conviction though, my 3 choices: India, Overpopulation, and Terrorist Proxies.
Religious extremism is waning in Pakistan since Zia's death.
Non-Indian foreign powers can't do much to Pakistan without Indian help.
Liberal? A joke? They are a very small part of the society and are needed in any healthy society anyway.
Economy: Linked with the war-threat/preparing to counter India and also to over-population.
Internal disharmony? No, Pakistan is far more internally united than it was even in its history.
IMO the biggest threat: water
Your list doesn’t haven’t it.
And more generally climate change WILL make a large part of this region unliveable within our lifetimes. We’ll lack the water resources for our population that we currently enjoy even in a limited amount.
Yes, and that is linked with over-population and to diverting resources to counter India. A small part of Pakistan's defense budget could be used to line up water canals, build micro damns, and indeed on educating people about water conversation.
As to 'corruption', nah, Pakistan's problem is not corruption. Corruption is a global problem, especially affecting many countries. And also, neither are Pakistan's politicians most in-apt in the world: If you want to see corruption and inapt politicians then go to Africa and Latin America where, despite no major wars, they are in real bad situation.
Most of Pakistan's problems boil down to the rivalry against India!