You definitely need to clear immigration, collect bags and clear customs at JNB, then go to domestic check-in. So any through-tagging of your bag is pretty pointless, as the bag will not go through automatically.

And even if you do persuade LHR to through-tag the bag, all that will happen at JNB is that the Comair staff will rip that one off and put a new one on.

I would strongly suggest that you don't book the 1040, as it's going to be on a separate ticket. I'm often on the 1110 (or thereabouts) to DUR. Usually, all is well, but even with the extra half an hour, there have been times when a glitch or two has made it very close indeed.