How many individual freedoms ought our government, reasonably take away in the interest of national security?

Which parts of the government should make those decisions, the elected officials or the career bureaucrats? Are there any freedoms that ought never be taken away, no matter what is happening? Should freedoms taken away be eventually restored? If so, how might those making that decision know when it is safe enough to justify returning them? If not, how might those making the decision justify the permanent arrest of certain freedoms?

NONE

None, because they don't have the right to legally take them away. They can appear to be taken away, but you must understand the supremacy clause of the Constitution to truly understand that they cannot really be taken away.

None. It is a false argument to equate security and freedom as a zero sum game. The more rights we have the more secure we are. Bush showed the fallacy of this argument. There are many including the Canadian Bar association who are calling for Bush to be charged for war crimes and crimes against humanity for his illegal actions post 9/11.

Those who would sacrifice their very real rights for the illusion of security deserve neither.-- Benjamin Franklin.

All the freedoms in the Constitution should be preserved, no matter the situation. If not, the state will chip away at them at every turn. It's not surprising that while most of us saw 9/11 as a tragedy, certain government officials saw it as an opportunity.

NONE.