It's my understanding that you cannot charge them for normal carpet cleaning, only the excessive damage, like stain removal, so you'd pay the regular cleaning fee, then charge them the itemized extra for the damage/stains. 

Purchase Price was $72k.The report reads as follows:Infestation 4- Excessive moisture conditions; wood moisture 23% in left and right front quadrant; 20% center.

Expenses in excess of the limit can be claimed only as an itemized deduction on Form 1040, Schedule A."

After thousands and thousands of dollars lost on make-ready and other types of repairs as well as time (money) lost on excessive turnaround time frames, I don’t believe that any longer.

Your first line of defense against loss is going to be insurance on the property, then an umbrella or excess-lines policy on the company. 

Definitely use separate accounts, whether you have an LLC or not.Checking: receive rent, pay billsSavings: hold deposit and reserves for capex, maintenance, taxes, insurance, etc.When your checking account has more money than is necessary to pay bills, transfer the excess to the Savings account where you can build funds for a new investment.

Not excessively. 

Do we leave that excess in the account after paying the mortgage?

It appears to me that you are being excessively conservative in your time periods per capital expense. 

You can make it clear to the tenants that they will be held responsible for excess damage or waste caused by the animal,  just as if they themselves did it.While you need to be careful to avoid a claim of retailation,   maybe schedule the next couple rent increases to be a couple percent more than you otherwise would,  and bank those funds towards expected greater turnover costs.