Of course, this assumes you're keeping track of everything religiously, as it would be hard to reconcile such records and ensure completeness.Otherwise, look into hiring a bookkeeper/accountant/CPA who can provide this as a service for you and can help advise you proactively, so you can prevent issues rather than remedying them after the fact.

Have to retrofit things, and abide by (or remedy) the structural decisions made over a hundred years ago.  

My question is, are there any other potential causes for this sewage backup, and anything else I should be thinking about that could make it much more costly than $1,000 or so to remediate?

The only remedy for the borrower is to catch up with the missed payments.. is there any other recourse here?

I only mention this because according to you he's "the most reputable person in the real estate industry and the most trusted and admired Bigger Pockets contributor":"its up to the owner to have them inspected quarterly and remedy wet spots or mold at the first sign..

The plan is to conduct mold inspection and remediation after the tenant moves out and then re-rent the property.

Protections for the Seller:**To protect the seller in case of default, the contract should specify the remedies available to the seller.

Neighbor wouldn’t remedy and city didn’t care.

What steps have they taken to remediate this for you?

Another option is to have the building tested, and if that is found you could get a quote for remediation.