Should we install furniture and furnishings before IAQ testing or flushout?

It's optional. In the past that has been unclear, and in an addendum issued 10/1/12, USGBC clarified that it is optional to install furniture and furnishings before IAQ testing or flushout for IEQc3.2. The word "optionally" has been inserted in the last paragraph of page 466 in the LEED BD&C reference guide, before "including furniture and furnishings."

Do the outdoor air minimum quantities have to be met for each individual space, or for the building square footage as a whole?

Ideally, the flush out will be designed to provide the minimum volume to each individual space, and the LEED Reference Guide indicates that teams must take reasonable measures to ensure there is no obvious short-circuiting of the airflow. However, the requirements only address the "total air volume," so, for LEED credit compliance purposes it is only necessary to quantify the total outside air volume supplied to the entire building.

I'm confident we have enough space allotted for recycling, but how much detail should I go into in documenting expected volume?

LEEDuser recommends providing a brief narrative that demonstrates you have estimated the volume following something like a Solid Waste Assessment. Resources such as those found at the California Integrated Waste Management Board can be useful. See case studies and approaches in the Establishing A Waste Reduction Program at Work participant's manual and in the waste disposal rates for Public Admin.