I'm not sure about the fines or fees. When it comes time to list the condo your Realtor will have to declare the Sq.Ft. source. You can use the public records as a source, your realtor can measure it out and declare it as measured or he can take your word for it and declare the source as the owner.
I can see how it might seem baffling that we've added square footage, but these are loft conversions with very tall ceilings (some as high as 21 ft), and a number of people have extended the square footage by creating rooms in an upper level.
As far as the building permit and fine stuff, I'm a licensed builder and can offer the following. Generally speaking, every town is different, but more than likely you will have to pay whatever the permit fee would have/ should have been + a fine that is equal to that base amount. That's how most of the towns work. Also beware that they could inspect it and find that something needs to be changed because you didn't do something per Code- then that would mess up your sale. Of course I can't officially tell you what to do- if you want an unfiltered opinion, please contact me.