We also underestimated the environmental component of the renovations leading us to have to expense testing we had not budgeted for and amend the project's final sow to work around those challenges Did you work with any real estate professionals (agents, lenders, etc.) that you'd recommend to others?

Would this be a lease amendment, or an addendum?

There are exceptions where you can do an escrow hold back if the "Cost to cure" is generally under $2K or you have a seller amendment to cover the cost and then they will hold it in escrow until repaired to release funds to vendor with proof or receipt.You have Fix & Flip loans but they an be a nightmare and the rates and points are excessive. 

I’ve received their report and filed for a LOMA, aka flood map amendment, due to what the specialist had concluded.

If you denied them housing because of their service animal, you are in violation of The Fair Housing Amendments Act of 1988.

The way we, who syndicate real estate deals for a living, protect ourselves from disgruntled investors with potential lawsuits is we COMPLY with Sec D 504, 505, or 506 of the Securities Act as amended.  

Reviewed all PSA, Amendments, leases, vendor agreements, title work, covenants Lessons learned?

Low-income rental housing for which a depreciation deduction for rehabilitation expenses was allowed.Low-income rental housing held for occupancy by families or individuals eligible to receive subsidies under section 8 of the United States Housing Act of 1937, as amended, or under provisions of state or local laws that authorize similar subsidies for low-income families.

Plans that are not amended as required are disqualified.

When the property is sold one typically cannot amend the lawsuit to New Owner vs Current tenant.