It never went anywhere and they couldn't provide me with an answer or guidance
That's easy to understand. The 2012 Guidance mentioned, the CTR FAQ's, and the SAR FAQ's all indicate it remains your option to use the occupation or type of business box instead. Your auditor cannot support its assertion because it is blatantly incorrect.
By using the "short list" John mentioned, FinCEN dumbed it down to the point where it is worthless. Moreover, from the NAICS web site:
The North American Industry Classification System (NAICS) is the standard used by Federal statistical agencies in classifying business establishments for the purpose of collecting, analyzing, and publishing statistical data related to the U.S. business economy.Individuals do not have a code; there is no matching them to either their employer or their occupation. Rather than being a "best practice," assigning an NAICS code to an individual is an indicia of ignorance.