500 km from Etosha to Windhoek is not a problem. Roads are good.
Aren't you planning Swakopmund? I really liked it. Make sure you are there on a Saturday to see the Snake Museum (or is it farm?) feeding. So much to do there and great seafood restaurants, wine... cheap too. Woman at the tourist office is a wealth of information. In Walvis Bay go sandboarding with Wayne from Dune 7.
Don't forget Cape Cross Seal Colony. Short day trip is plenty. Can do it from Walvis Bay to Spitzkoppe. Just keep going north of Henties Bay then double back to Spitzkoppe Rd.
Naukluft - I did the Waterkloof Trail and it was OK but it is a good place to stop between Walvis Bay and Sesriem. There are kudus and small antelopes near the campground which is pretty cool.
Spitzkoppe is beautiful but I think one night is enough if you arrive before sunset and leave after sunrise. I really wanted to summit Brandberg but did not have time. Ask about the drive to the coast on the SW of Brandberg close to Uis. Something else I wanted to do but didn't have time. There is camping near there but the name of the site escapes me.
I think you could omit south of Windhoek unless there is something specific you want to see. I went to Fish River Canyon and was not overly impressed but I've been to Arizona and Utah which frankly blow Fish River away. And you can't hike anywhere without going through massive red tape. They simply don't want people hiking for (justifiable) fear of a rescue. I heard Luderitz is nice but I did not go.
Try to fit in a trip to the Okavango Delta in Botswana although it is a bit tough logistically since you already have the campsites booked. Shame to miss it since you are so close and have time. If you go, then forget the complacent, lousy, overpriced service of Audi camp and go with Old Bridge Backpackers. An overnight in the Delta is awesome and you will do game walks getting very close to zebras, buffs, and eles. Old Bridge also arranged a scenic flight over the delta which was a bit pricey @ $75/pp for an hour with 5 people but it was really good.
Jon