That no additions or remodeling was completed without a permit.

I am glad because the permits and requirements would have much tougher.

Only thing better would be initial deposit and then paid in full upon Certificate of Occupancy and punchlist complete.Of course, standard items should also be checked: licensed, insured, willing and able to pull all required permits, reference checks.I would also commonly avoid the cheapest bid you get.  

We also learned that the house had failed or not received many of Baltimore city’s permits and inspections.

Duplex have different zoning that may permit additional units.

Is the property priced appropriate for a purchase that does not permit financing?

As long you work permit visa (H1B OR F1 etc) then you will be able still get qualified with a conventional loan.

I still don't have permits after a fire and things were submitted in March for applications.

Your HAP Contract certainly won't permit the Section 8 tenant to be charged and she will complain.

Currently, the contractor is demanding $44K upfront to resume work and complete the occupancy permit, promising to discuss the additional costs afterward.