HELP -- Huntsville AL Flipping Laws

I am underway on my first flip.  This home is a simple paint, floors and kitchen cabinets.  I received a stop work order, and had a inspector walk thru the home.  I am being told that "this amount of work has to be all done by a contract."  Apparently any reno over $250 (labor and materials) I will need to have a general construction permit....Even if this was only painting I'm over $250.

The big sticky point seems to come from the "gutted" kitchen, and installing cabinets.  She is adamant that this MUST be done by a licensed professional.  Also the re-installing toilets (removed for tile demo), and hooking up dishwasher must be done by a licensed plumber/electrician.  

I think my lesson learned is apply for general construction permit with all working cabinets/appliances in the home.

Does anyone have any advice for me on this, as I prepare to meet with her boss this afternoon?  

Thank you all