If one has no real nusach as his father was non-jewish and converted but his mother is fully Jewish is one free to choose ? Secondly I am studying books on the Vilna Gaon, can I follow his minhag as he has a siddur that he arranged and created ?

A convert may chose the nusach he /she is most comfortable with. I would not be hasty to chose a nusach that differs greatly from that of the congregation in which you regularly daven, but the bottom line is that you may choose.