Lenny, I think you are picking wisely. Namibia is a great place to start your African hunting. I say "start" because once you go; you'll always want to go back.
We flew through J-burg SA on our trip to Namibia. We actually spent the night in J-burg at a wonderful bed and breakfast. The down side of that is that we had pick up our guns and then recheck them when we flew out the next morning to Namibia. As much as we loved our stay (going both ways) at the bed and breakfast, it will save you a lot of red tape to book right straight through to Namibia. That way you won't have to hassle with your guns in South Africa.
Namibia is a wonderful place to hunt and explore. There are several top notch PH's and most of them will accommodate you in hunting as well as side trips. Their service is superb and hospitality unmatched. We saw lots and lots of game and I took some great animals. Relatively speaking, Namibia is probably the least expensive place for an African hunt.
You can either go through an agent here or straight through the PH. I'm sure others will share a good PH with you and I'd be more than happy to do the same. If I went back, I'd go to the same hunting ranch as I know of their wonderful service and great animals. (You can read my story "Se ah bra" about my trip to Africa under the section here of stories) Or, if you want to contact me personally, I'll send you a copy of my complete journal covering everything we did for 12 days. If you're interested, I'll put you in contact with them to see if they are booking for 2012. If I knew I was going, I'd definitely book as far in advance as possible and lock in the prices.
My email address is firstname.lastname@example.org