I have seen the existence of oil tanks not be remediated properly, and it end up costing a developer $500,000 to remedy the situation, including the environmental impact and the cost of fees and penalties levied against them. 

You would generally never have a reroof job, just maintenance every 10 years where you remediate blisters, fill low spots and apply a new coat of elastomeric.

As @Shawn Dandridge has pointed out, you have legal remedy through the U.S. court system.

Hopefully remediation costs were factored into your purchase price.

According to the township if I bring them my time line, cost, and scope of work to remedy the work they may be able to negotiate down the fines, but there's no guarantee of this.

Good deals usually come with things that need to be remedied so you have to decide if you're willing to pay a few hundred $$ more or a couple thousand more to deal with the mold? 

If there is a basis then you will need to remediate but I would be clear to the tenant that if there is no basis that is the end of it. 

Tenant agrees to a new termination date of the lease of July 31, 2015....Landlord agrees to refund to Tenant all unapplied pre-paid rent less costs for damages, utilities overages, cleaning, and financial remedies upon the date Tenant quits and vacates the property.Would you recommend billing the tenant for the damages from Question #1, or go ahead and deduct the amount for damages from the rent refund just as the tenant signed and agreed to in the Early Termination agreement?

Adequate liquidity levels held by large and complex servicers will minimize the likelihood that financial downturns have an adverse effect on these entities, and provide regulators more options in the event that severe problems necessitate regulatory remedies.

IN SUCH EVENT, ESCROW/CLOSING AGENT SHALL RETURN TO BUYER (AS BUYER’S SOLE AND EXCLUSIVE REMEDY) THE EARNEST MONEY DEPOSIT.