We spent 3 months in southern Africa last year including Namibia and Botswana. Traveled with a small truck and camper (15,000 km). Best experience of my life.
So a couple comments. First, roads in Botswana are excellent. You will have a much rougher ride in Namibia if you get off the main highways and onto gravel. Some of these are excellent, others not so much. Read my road reports at http://www.lifewellspent.com if you want to know specifically which are bad.
The Skeleton Coast is not worth it. Most of it is socked in with fog. Even when you see it, it is not scenic. Flat rock-strewn shoreline with flat grey ocean rolling in. Probably the most boring drive of my whole life. Also, your rental company will have it on the no-go list so you will be driving without insurance coverage if you do it. So it's a risk for nothing, really.
Yes, it costs $1000 R to cross borders plus fees at the borders. See road reports for specifics.
The Okavanga Delta has been the highlight of my traveling life. We arrived in Maun, went to Wilderness Safaris (across from airport) and asked if they had any last minute deals. We were offered a choice of five different lodge trip (2 nights each) that were leaving in the next week. Price was about 50% off because we were in the country and ready to leave. We chose to lodges/locations, hooking them up to make a 5 day, 4 night trip. Included were the three flights - about 2 hours total flying time which was costing people $300 US per hour just to do fly overs. It was a great deal and hands down the best experience. But read the report if you are interested. Just go to website and scroll down to Africa then choose report you want to read.
Sossuvlei needs at least three days. There is the day you arrive and set up camp in the evening. The next morning you get up before sunrise so you can be on the dunes for sunrise. Enjoy the morning, sleep in the afternoon, enjoy hiking the dunes as the sun sets. Leave the next day.
Don't waste your time in any of the cities. They really are not worth your time. Especially Gabs. Get in and out ASAP. The one exception would be Capetown. Looks like you are just going there to fly out? That is very sad. So much to see in that area.