Collecting a damage deposit is a core task of a PM that you pay for and they either failed to do it, or failed to properly record it... either way, unacceptable.   

How do I know how serious the foundation damage is?

The value of the property has a direct effect on the amount of leverage that can be geared for that property to ensure a particular rate of return for investors. 

The net effect will be, you will get to deduct 1/2 of self employment tax and full health insurance expenses.

After inspections I was able to get a $3000 repair concession effectively paying my $200k initial offer!

I feel that based on my interaction with them, that they would be responsible pet owners, although pets always incur a level of damage.  

My concern is damage and changes of tenants. 

It stated in effect, that CAMs would be prorated over the then leased area, not the percentage of GLA that our unit represented.

It's hard for me to imagine pet damage that extensive though.I'm wondering if the smell penetrated into the insulation behind the walls at the lower levels and if it's getting into the new / cleaned areas and "reinfecting" them?

Definitely check all windows, ceiling, roof for water damage.