I let this sit for a while and just came back to it today and figured out a solution. My issue was with Saving and Opening.
Saving: I'm guessing that by saving the file directly from a String the platform takes away the New Lines when using a FileWriter wrapped with a BufferedWriter. To fix this, I just forced new lines with custom code.
Opening: When opening the file the New Lines were also removed so again I just forced new lines with custom code.
Here's the working code.
This isn't the finished product: change things like remove the Output Points and condense the number of String variables in the file.