But hold on to all communications with them regarding this beause if this goes ballistic, THEY have a great deal of liability in this.2) As @Nathan Gesner said, get a new Mold Remediation Company and have them go over the entire house 100% and re-treat it, then give you a written certification that it is safe and clean.3) Get rid of your brother too.

Most fail to take this last step, or merely obtain insurance certs where they are listed as a certificate holder. 

I sold a property last year that required the owner to get a certificate of nonconformity to be a legal two family.

A good way to avoid this in this future is to use a vendor worksheet/package that request the pertinent contact information along with a document request for the filed out W-9, copy of business license, Worker comp and liability insurance certificates.

Hello everyone,we got a bid for 20k to get our rental property ready for the market and get the CoO (certificate of occupancy).Any product out there to finance the project?

They city will red tag it and require you to upgrade everything and get a Certificate of Occupancy before you can rent it.

And then I applied some leverage knowing that if they did not want to move forward that I would find another interested Buyer who was clearly ok without having the Certificate and knowing it was always used as a 2 family. 

One reason could be that not all appraisers consider basement space to be "general living area" (GLA), regardless of the building codes.To overcome this barrier, you can:Provide Documentation: Present the city’s approval for the egress window and any other relevant permits or certificates that show the space was done according to code.

As an investor-focused agent in the Cleveland market I always have my clients write the following contingencies in when buying a house that's tenant occupied:1) Offer contingent on home inspection- usually a 7-10 day contingency period, this contingency allows you to either A) move forward with the deal B) renegotiate the price if issues are found, or C) walk away from the deal2) Offer contingent on appraisal if you're going financing3) Seller to provide copy of current lease agreement4) Seller to provide a rent roll/tenant ledger with proof of payments received5) Seller to provide copies of 3 previous months of any utilities paid by the landlord6) Seller and tenants to fill out Estoppel Certificate.

I will soon graduate college with a degree in finance and accounting, I hold a PMP certification along with a few others and plan to work on my real estate license and maybe in the next couple years obtain a residential contactor license.