Okay so solution was to make the Objects in C# and Serialize them using "JsonConvert.SerializeObject()". Rather than constructing a string which is prone to error. So the new code looks something like this

                   //create new element to be added
                    var lst = new List<Element>();
                    lst.Add(new Element() 
                    { 
                    name = node.Name,
                    udi = udi
                    });
                    //create new elemnt wrapper with propoer relationship to be added
                    var obj = new RootObject()
                    {
                        name = "Item " + (nestedResult.Count + 1),
                        ncContentTypeAlias = link.ncContentTypeAlias,
                        relationType = type,
                        linkedElement = JsonConvert.SerializeObject(lst)
                    };
                    nestedResult.Add(obj);
                    nestedStr = JsonConvert.SerializeObject(nestedResult);
                    if (isNew) 
                    {
                        linkedContent.SetValue("linkedElements", nestedStr);
                        sender.SaveAndPublishWithStatus(linkedContent);
                    }