Thanks for your help. After seeing your reply, it led me to do a little bit of more research. You pointed me in the right direction.
I Googled the City's Building Department, after speaking with a Senior Builder he gave me insight as to the whole process on the obtaining my CO (certificate of occupancy) for the non-permitted 2 units. First off, contact the City's Planning Dept, provide them with the properties address, see how the property is zoned. One crucial piece of information the Planning Dept provided me with is that if the buildings are located anywhere within the property lot's "setbacks" (specific square footage adjacent to the property line), the city would not allow the buildings to be permitted, and could even order them to be tore down. Right then and there, that could be a deal buster. Now, if the two units were built outside the properties "setbacks", that would be ok.
Secondly, The Building Depts process is first to submit a floor plan of the units, anyone with drafting skills would be able to complete one. Second of which, have an inspector view the property, in order to deem it safe. Fee for 2 hrs of work, $250. The city will also impose a building fee, even though the units had already been built before you acquired the property, they'd have to be paid in order to have the units permitted. The fees are public information which I found on the Building Depts website, easily you calculate how much square footage the buildings are and you pay the building fee, for my case, the two units come up shy of 1000 square feet - totally my building fee to approximately $10,000!
All in all, the expense to have a building permitted would cost approximately $10,000 - $12,000. Good negotiating bit of information to present to the seller, maybe ask for a credit.
It's always best to do as much research on a situation like this where it could end up costing you thousands of dollars out of pocket. It's always good to ask for advice and have someone point you in the right direction. Thanks!