There were no true comps and the appraiser gave the permitted ADU no value as a unit or even as livable sq ft. 

Went over budget because we hand a lot of custom additions to make it unique and stand out.

What is the key trait that would make a customer want to live in this property?

Namely timing, cost, and getting permits and such. 

I've dealt with a lot of permitting and zoning issues, which are never fun or go the way you planned. 

I assume I need to apply for a permit but I'm not sure of the alterations that were made (what walls were originally in place or new wall that were built to convert it to single family).

There were open permits for the work done but the title company was unable to find the CO.

I am Connecticut raised, received a degree in architecture at Wentworth Institute of Technology in Boston, Massachusetts, and have been living and working in architecture in Denver, Colorado for four years in June 2020 with experience in developer driven SFR, Duplex and Multifamily as well as custom single family residence design and project management.

As a flipper, you will need to know a lot about managing jobs, proper construction techniques, permitting, inspections, building code, etc. 

https://www.sanjoseca.gov/business/development-services-permit-center/accessory-dwelling-units-adus/adu-amnesty-programAlso, you could try speaking with a local architect like @Adam Mayberry.