This is specific to Magento 2.1, but knowledge on other versions may help in pointing me in the right direction.
I have tried a few things and have scoured the internet for similar solutions but most have not been answered or are for previous Magento versions.
I have an existing standalone website that was completely custom built that uses PHP, HTML, CSS and JavaScript and almost all files are '.php'. This existing site is not on any platform and is not 'E-Commerce'. The existing site is visually how we want it, it has a custom dealer locator, custom json and other data retrieval portions. I want to take these files and structure, preferably exactly how it is, and use it as a E-Commerce site that is integrated with Magento. By Integrated I mean having the ability to call Magento's functions/methods so I can use Magento's tools such as creating and editing accounts, shopping cart, checkouts, etc.
Thus far, I have created my own custom theme in Magento, created custom modules and neither of which seem to give me the capabilities of what I am looking for (or else I have misunderstood the documentation and need to expand). Magento uses MVC structure and I would prefer to not use it if possible. The current format I have my site in is in the structure below.
Above is how I built the existing site and it is structured how we develop. In what direction should I go in order to achieve this custom development structure within Magento while being able to use Magento tools?
My question is very similar to this post, but I would like to use the Magentos tools in a more direct way and potentially exactly how they already exist. Using Magento as backend ONLY for website
I will elaborate, add code, answers and questions as fast as I can upon a request.