Why couldn't you get a visa for SA? I am guessing you did not realise that people residing in Botswana are among those scheduled for Jhb?
In response to your questions...
I can't say for certain but I can speculate:
I had my interview in Jhb and there was some time period between when KCC said they sent the file, and Jhb received it - it wasn't an urgent matter for me so I didn't really keep track of the timing though. Maybe this means that KCC are still sending hard copy files to some consulates?
Also I am sorry to tell you that you will not have priority at all but will probably go further back in line. KCC will not be involved in scheduling your appointment at all from now - it will be up to Nairobi and when they can fit you in. KCC scheduled initial appointments but after that has nothing more to do with the cases and any further issues including rescheduling are up to the embassy or embassies that you are dealing with. So nairobi must wait for Jhb and then you must wait for nairobi. People requesting transfers of interviews in the past have often had to wait for a few months I'm afraid
Maybe you will be lucky and Nairobi will have a slot available sooner...
By the way I never had an issue with Jhb returning emails - sometimes a delay of a couple of days - but it is the midst of the main holiday season in SA at the moment and they may well be running on skeleton staff. It may be more fruitful for you to call the consulate and speak to someone there.