Unpermitted Addition, Stop Work Order, Bad Idea?

[Nicholas LaGatta]

I am interested in buying a property in a historic district, shut down for not having permits.  They put a 1000 square foot additional in the back, which appears to be quality work to code, but there are a few minor issues to correct to comply with historic regulations.  

I could have great economics with this deal, even if I paid a contractor to do the job correctly start to finish and straighten things out with the city.  

What are the risks involved?  If everything is to code, I hope it's just a matter of paying any fines and starting the paperwork from scratch.