Managed to solve it myself.
So here goes,
Step 1. I had to remove commented code from my php file as it was breaking through somehow, thats where the came from at the end of the JSON array.
Step 2. I had to remove an additional echo from the php file which I was using for error checking. I think I'm right in saying the only echo you want to have is the json_encode.
Step 3. Checked the length of JSONarray in Java and it was logging 5 so I now knew it was reading correctly.
Step 4. Added Pavneet_Singh's code snippet to replace
Step 5. Converted stringList from an ArrayList to a String array using this code
stringArray = new String[stringList.size()];
stringArray = stringList.toArray(stringArray);
Happy days! I've spent far too long trying to figure this out haha the first two steps are pretty noobish but it's sometimes the most obvious things in life that are the hardest to find. Hopefully this can help someone else too!