I've driven Cape Town to Durban several times using the N1-N5-N3 routing, and will be doing so again on Friday/Saturday, so perhaps I can give some pointers.
The N1 between Johannesburg and Winburg, I have never driven and have no knowledge of. Winburg to Bloemfontein has frequent passing lanes and shouldn't be too problematic.
The stretch between Bloemfontein and Colesberg is where I've experienced the most issues with overtaking trucks. It was also undergoing significant maintenance (lengthy stop-go controls) when I last drove it (December 2011), but that should be done by now. The rebuilding of the N1/N9 interchange in Colesberg is also complete to my knowledge (a significant danger zone previously).
At Colesberg, the majority of the trucks head to the Eastern Cape via the N9 and N10, and you'll probably end up with the road to yourself as far as Three Sisters. Be very aware of fixed and mobile speed traps though, especially in the Richmond area (the road may be empty, but don't even think about exceeding the speed limit; you will get nailed heavily). The truck traffic between Johannesburg and Cape Town generally uses the N12 via Kimberley to avoid tolls, so you'll hit this from Three Sisters onwards.
The stretch between Beaufort West and Laingsburg is, in my opinion, the most dangerous stretch of the entire journey; fatigue being the reason. If you're even remotely tired, pull over and rest (or even stay in Beaufort West overnight if you have to). There's a Shell Ultra City at Leeu-Gamka (halfway through this stretch) that I recommend you make use of.
(Pull off at Matjiesfontein, 30 km after Laingsburg. Well worth the visit.)
From Laingsburg, you just need to get down Hex River Pass (again, keep to the speed limit here), and get through Du Doorns (the one section where the human population may have hostile intentions). Then it's a blast through Worcester, the tunnel (keep to the speed limit in and after the tunnel; in particular, fixed cameras approaching the toll plaza right where it drops to 60 km/h), and a short skip and a jump to Cape Town.
Enjoy the trip!