This could be for several reasons like the Seller filed Bankruptcy, the Seller requested a loan modification, the Seller notified the lender of their intent to sell, etc. 

Since all units are located on the same land and considered one property how can I verify these dwellings are up to code and won’t require costly modifications after purchase?

If they can only produce a LNA, discount it heavily and plan on doing completely new docs  (modification or new note).

(Or what level of finish, improvement, or modification do I need to make to maximize a property's value or performance?)

He can also follow, and see when that loan becomes 90, 120, and if the loan enters into a modification or mitigation status. 

They can reinstate, potentially receive a forbearance plan, or a loan modification.

(As with everything with tax laws there are exceptions and modifications to that rule.)Not sure what "I didn't file anything until 2016" actually means, and that could be important.

But when rehabbing properties, I prioritize installing parts and modifications that allow for easy repair and the minimization of emergencies. 

If you have any modifications you think I could make that would be really appreciated as well haha!! 

It’s likely that any issues can be addressed at the time the loan is originated by either negotiating the loan covenants to allow what you intend to do in the future, or by writing the operating agreement so that it is in final form and all you need to do later is the PPM and subscription agreement, with no modifications necessary to the operating agreement.