What can I do to the existing structure physically or in a contract to reduce liability?

Greg,Always a concern on dues, special assessments, what type of board members do they have, are they physically sound?

Then you do not have to go into a physical classroom and you can handle everything online and get all the courses done in 45 days. 

Thus, I need someone competent to do a thorough financial analysis to help me understand where the swing points are in the tradeoff where one option would make more sense vs. the other one.Something along the lines of:https://www.nytimes.com/interactive/2014/upshot/bu...but which also incorporated my current investment property holdings.

Good that you bought it as an LLC, because it sounds like a law suit waiting to happen.If I'm reading this correctly, my recommendation would be to encourage the tenants to move, then start over with a new design, making sure to incorporate someone who knows a little about building codes. 

My name is Brendan I am a Physical Therapist from Mahopac NY.

Also do they rent a physical space or own it?

Were the later materials actually "incorporated into the house" (I assume they were not acting in any way as just a "material supplier" so simply buying them and even delivering them without installing them would not count as work).

Buyers that do not have physical boots on the ground often get taken for a ride -- see for example the "turnkey providers" and various threads lamenting that experience. 

A $48,000 quote is so ridiculous I am hoping you have a physical copy of it that you can post for us to see.