@Kevin Nerio You would most likely need to go through the re-zoning application process. The city will not approve permits for work until the property use is brought up to code. It's not as simple as paying off violations for previous un-permitted work. If the property is not zoned for sing-family use, but you are using it as a multy-family, you will continue to receive violations until the county approves the application for rezoning.
Miami-Dade also just passed an ordinance (Read about it here) to allow additional dwelling units(ADUs) on single family zoned lots, allowing the owner to rent the ADU, requiring the owner to live in the main house. This new ordinance allows for just one ADU per property. So if you can reconstruct the house to be a single-family, with just one ADU, and you are willing to live in the house that could be you best bet at saving your investment.
Another option could be to contact a construction attorney who is involved in projects requiring more complex permitting or zoning applications. I have found some interesting contacts by searching properties here and following the links to zoning applications for similar properties in the same area. Happy to walk you through this site and share with you how I use it and other ways to find out what you can do on a property. Feel free to DM me.