Bob,
The problem with transfering through Cape Town is lack of a secure baggage storage area. Johannesburg has this and you just transfer yourself. Cape Town was supposed to get a secure area three years ago.
When I was there someone from the police took the firearm cases from the baggage carousel to the SAPS office. There we did the forms and inspection. Then I was issued a permit good for 24 hours. I think the form are vastly more complicated. There is a service you can hire to assist you. I think the forms can be downloaded.
You return the form and they handle the transfer of your firearms to the plane to Windhoek. You have to rebook all your luggage and sit with it for a few hours. It's a real pain.
John
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