@Nick TalaricoAs suggested - it helps to have a separate bank account for just your real estate related activities.This way you know 100% of the activities within the account are related to the real estate related activities.You can export the information into excel and properly categorize the information.One you scale up, you may want to consider having an accounting software such as quickbooks, Stessa, Quicken, etc.

House was poorly configured with multiple additions and never properly laid out.

You will already have made money "purchasing" it, so your initial capital at risk is $0, just added liability and future major costs, which are likely mitigated by builder warranties and proper insurance.Make sure you have all numbers correctly considered, do your due diligence and ask yourself what the worse case scenario is. 

Find out when he's home and stop by-bring another family member along.I know you've sold it, but for future reference, you don't need his permission to enter, you just need to give him the proper notice-usually 24 hours.

Learn how rentals work with this first investment, DIY as much of your own maintenance and property management as you feel comfortable with, get your feet properly wet and your hands property dirty. 

If you have not established the proper relationship with them or they don't have anything to authenticate or verify you yet, an email is not worth anything.

I agree with the others that it is the end result (i.e. does it look right and function properly) that matters most, not so much a piece of paper.  

How you want to proceed is up to you, personally I’d inform them that they did not follow the proper process by getting the animal before receiving your authorization, and therefore their ESA designation is not legitimate.

The mortgage is still in sellers name until some time in the future. 1)How do I or how am I properly protected if my Seller dies?

We don't believe we necessarily need to form an LLC for this initial investment but would love more in sight into the proper process of pulling this off.