Over the winter I added a zero offset seat-post and aero bars. I noticed every time I road on the trainer my right hip felt weak the next day. Since I started riding outside it has increased in pain. I know I probably should post pictures but i want to know if this pain could be a result of the new position. The new position does feel really comfortable and my hip doesn't hurt during the ride.
Adding aero bars and not moving the seat forward will close your hip angle, causing a loss of power and possibly difficulty breathing deeply. Post pics, but I think you need to move the seat forward as far as possible, or, more likely, need a Fast Forward seat post.