They assessed them as "two single family dwellings" and also declared both houses to be non-conforming. 

If so, that will turn away a lot of potential buyers, they don't want to have to conform to the house, they want to be able to move into a home that feels comfortable to them.3–To whom are you marketing the property?

Most conforming loans are the same. 

Since you aren't occupying the property, it's an investment property so an 80% LTV refi for a 4 unit is non-conforming.  

Even though they may be personal property(depending on your state), my guess is it will be non conforming for FHA

If you're a conservative investor, conforming loan is always the best choice, as it allows you to get a very low rate for investment properties.

In my market, additions are typically not worth the extra cost, and work, and they normally dont fit well with the property, however if they did a good job, and the property still conformed with the neighborhood, I would imagine that it would add a decent amount of value. 

Converted a non conforming den into a bedroom, landscaped the backyard, added tile throughout (except bedrooms), and a beautiful tile backsplash!

Maybe talk with them before getting too far into your development otherwise all your efforts may not get you a legal, conforming property. 

Today's conforming wholesale rates for 30-year money were 4.076%...even if there is a modest bump money is still free in real terms to me with the real CPI hovering around 6%ish according to Shadowstats.