This last May was my first time through Joberg and then to Port Elizabeth and I used a agent for the permits and transfer, I would highly recommend for you to do it also if you are a first timer or even a savey traveler thorough Joburg.
If you use a agent they will meet you right at the plane and whisk you right through all the lines and they will have your pre apporved permits with them. The agents that I used also met me on my return flight from PE at Joberg after I had picked up my rifle and suitcase and wisked me back through where I needed to go and left me at the security checkpoint. I did pay extra for a meet and greet and it was a great experience with no problems at all.