I drove Cape Town to Durban using the N1-N5-N3 route in December (and back again a few weeks later).
It's ~1,400 km that you'll be driving, which is a bit of a stretch for one person to do in one day, so I recommend that you break the journey. Colesberg is my usual place to stop over; quite a lot of B&B's in the area for people on roadtrips stopping overnight.
In terms of roadworks, the stretch between Bloemfontein and Trompsburg is being rebuilt; there are three Stop/Go sections and you can find yourself waiting for up to 20 minutes at each one. In fact, on my drive, there was a truck accident along that stretch as well (which I was warned about before leaving Colesberg), so I took a detour using the R704 and R706. That may be an option for you as well. There's also resurfacing of the N1 between the Dwyka River (~15 km south of Prince Albert Road) and Laingsburg where you may also experience Stop/Go controls. I also believe that the N1 is being (or is about to be!) realigned through Ventersdorp, but as I didn't pass through there, I'm not 100% sure.
You won't experience that much traffic. Most of the traffic south of Johannesburg will disappear at Bloemfontein, and there'll be a few heavy vehicles south of Bloemfontein through to Colesberg, where they head off down the N9 to Port Elizabeth. Most of the truck traffic between Cape Town and Johannesburg uses the route via Kimberley to avoid the tolls on the N1. (This route can be considered; it's not much longer in terms of distance than the Bloemfontein route, but can be considerably longer in terms of time.) Most of the time between Colesberg and Three Sisters, I have the entire road to myself. Even when there are heavies on the road, they tend to be far between (it's nothing like the N3!), so you won't be stuck behind one for any considerably length of time.
Just be aware of the speed limit reductions in and around the small towns along the route; expect to see speed limits of 60/80 km/h as you pass through them. There are plenty of cameras (both of the fixed and the "Koos hiding in the only bush for miles in the Karoo" variety -- and those guys camouflage themselves extremely well!), so don't even think about exceeding the speed limit unless you enjoy paying speeding fines.
You'll find tolls at Lenasia (the Grasmere plaza), the Vaal plaza just south of the river, and at the Verkeerdevlei intersection between Winburg and Bloemfontein. Once past Bloem, the only toll you have to worry about is paying to travel through the Huguenot Tunnel (there are new fixed cameras just inside the 60 zone before the plaza, be VERY careful about those), although you can always take the old pass over the mountain if you wish.
Anyway, hope this helps.
