Depending on the damage, a good soda blasting will remove a lot of the soot, char and odor. 

I've also charged the tenant for the cost of professional cleaning and odor removal, but then applied the money towards replacement flooring costs.

Dead animal odor will typically go away after a couple of weeks.

Cats are quiet, but the odor can impact the neighbors and destroy an apartment if the Tenant doesn't take care of them properly.If you allow them, what do you do to mitigate your risk?

Must have been more odor in the nooks and crannies of the windows (with those pane bar things) than I realized.  

The odor is back !   

Sounds like, aside from the odor issue, they've been paying on time and haven't really given you any issues as an inherited tenant until now.

Kilz also makes a low-odor version, works almost as well as the regular stuff.

Even if they swear they'll never smoke inside, they will, and will drive your other tenants nuts and it's expensive to get the odor out.Get your tenants to pay online so you aren't chasing the rent check.Be direct with tenants. 

The appeal is truly story time, I enjoy it because I get to put on my "grumpy old men" persona and grumble about everything that detracts from the property's value.Hope this helps!