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. 

Let me know if I am missing anything.Purchase cost of an old house on a 7,000 sq ft lot        - $ 1,800,000Architect Fees                                                            - $     30,000Other Soft Fees (like Permits)                                     - $     45,000Construction (3,000 Sq Ft)                                           - $   700,000Finance Costs(Borrowing around $1.4 m for 2 years      - $   110,000as primary residence mortgage)Selling Costs (5% of $3.3 mil)                                       - $   165,000------------------------------------------------------------------------------------Total Costs                                                                 - $ 2,850,000Selling Price                                                               - $ 3,300,000Profit                                                                         - $    450,000Are these realistic?

When I tried to pull permit for an addition, the city asked the issue to be resolved before permits can be issued.

Let me know if I am missing anything.Purchase cost of an old house on a 7,000 sq ft lot - $ 1,800,000Architect Fees - $ 30,000Other Soft Fees (like Permits) - $ 45,000Construction (3,000 Sq Ft) - $ 700,000Finance Costs(Borrowing around $1.4 m for 2 years - $ 110,000as primary residence mortgage)Selling Costs (5% of $3.3 mil) - $ 165,000------------------------------------------------------------------------------------Total Costs - $ 2,850,000Selling Price - $ 3,300,000Profit - $ 450,000Are these realistic?

The entire structure has been revamped with no permits, no requests and no approvals which the CEO (Code Enforcement Officer) didn't appear they would give them."

Sec 34-863 & 34-864 covers not getting a permit in the first place:Sec. 34-863.

@John Underwood in certain counties in TN like Davidson (nashville) you cannot get owner occupied permits in an LLC.99 % of owner occupied permits are for Residentially zoned properties.

I have a SFR in a rural area that doesn't have permitting requirements.

I have a SFR in a rural area that doesn't have permitting requirements.