It may not make a great deal of sense to you and I, but you're forgetting to add religious zeal to your calculations.

Given the Pakistani military's long standing and often demonstrated distaste for religious zeal, I don't see how that would help the calculation.

I think that the Paki military is split along religious lines to be fairly well demonstrated.

Demonstrated when? How? I can see a split between the anti-terror and the anti-India sides of the military, but I don't think either side would be naturally aligned with Iran, especially not on religious grounds.

Why would Iran want to fund the Pakistani military? Would it even be capable?

It may not make a great deal of sense to you and I, but you're forgetting to add religious zeal to your calculations.

And anyway, they don't need to fund all of them, they simply need to influence some of them... and I think that the Paki military is split along religious lines to be fairly well demonstrated. Would it be to Iran's advanatge to be formenting that split, do you think?

Is the concern that the Pakistani military would convey the nuclear weapons to Al Qaeda or that some of them would get into the hands of Al Qaeda in the chaos following the collapse of the Pakistani government?

Presumably the latter, given al Qaeda's and the Pakistani security forces mutual animosity.

I'm still unclear as to how al Qaeda will manage to rest control of those nuclear weapons from the Pakistani military.

Is the concern that the Pakistani military would convey the nuclear weapons to Al Qaeda or that some of them would get into the hands of Al Qaeda in the chaos following the collapse of the Pakistani government?

Iran roars to mind.

Why would Iran want to fund the Pakistani military? Would it even be capable?

If the state collapses, who will be paying for the Pakistani military?

Iran roars to mind.

If the state collapses, who will be paying for the Pakistani military?

The same people who are paying for it now, Pakistani tax payers. It's not like military rule is untried in Pakistan, they seem to have gotten quite good at it. I certainly see it as a more likely outcome than a Taliban-style regime.