When you buy a primary residence you are typically using a conventional conforming (fannie/freddie) type loan.

Here in Colorado, we create a lot of non-conforming duplexes out of traditional single-family homes.

I would look at people that are handyman over anything else, contractors will be used to getting more money and the amount you would pay them would either be too low, or the they would not conform to your work/company.

The meters, bills, old permits (should be available through the city planning), the appraisals, etc.Most appraisers check with the city on permits and non-conforming use while doing their research. 

Did they require you blueprints and plans be reviewed and made to conform to their standards?

You won't be forced to de-convert unless you have violations...eventually the city will start fining you.Very critical terms are non-conforming (no violations - grandfathered in) vs. illegal (violations)...

Non-conforming/portfolio loans, which aren’t conventional loans, will allow as little as 20% down. 

@Kevin Collins you are asking for advice and I am taking time out of my day to actually give you a different view point in an attempt to help and assist you but you are upset it doesn't quite conform and confirm your thoughts in the way you expected. 

If its a conventional conforming loan then I believe they should be reporting your payments.

Commercial zoning would be okay as long as the property is considered LEGAL but non conforming.