Hi, my rental management company collects one time non-refundable pet fees and monthly pet fees from the tenants.

now many attorneys write title insurance and have that practice but one who is not an agent for a title insurer should have known better and so had your lender.

Actually, these properties don't come up too often so there's practically no comps.They are cash cows and the owners know it so they charge a lot more then the house would typically be worth. 

As far as your actual mathematical calculations, yes it is all right except for:1 - your Cash-on-cash you are correct in it being 13.29% if you do not factor in closing costs however, if you factor in 3% ($4,008) closing costs your cash-on-cash is 11.56%2 - you cash flow of $296 is mathematically correct however, understand that your property management will be based off of collected rent and if you are factoring 10% vacancy the correct way would actually be to factor your PM fee after vacancy is accounted for because again most PM fees are on 'collected' rent - so if you run PM AFTER vacancy your PM fees are 1,728/yr. and in turn your cash flow is actually $312/mo. ($3,744/yr.).

Tenant either didn’t pay it or bad landlord practice of including it in the rent.  

She obviously had no idea what normal practices were. 

Wheelbarrow Profits by Jake Stenziano and @Gino BarbaroHands down the most practical and down to earth book on multifamily I've read

I've been provided by the seller what appears to be solid leases.What're some best practices in this type of transition? 

They are merely a way for the town to track construction for the future and to collect money.

The realtor has become increasingly unprofessional and yesterday accused me of concealing the issue, and "of faulty workmanship and or lack of proper building practices and the renovator should be responsible and cover the cost of this repair, whatever the solution is."