If this is still relevant - I am not really an expert, having never taught at Wits myself, but have been affiliated as a visiting researcher in the recent past. I would be looking at:
1 - funding formulas, esp the subsidy system of rewarding academics financially for publication (see for brief explanation this news article:
http://mg.co.za/article/2011-02-25-publish-or-be-damned). The NRF is a (the?) major funding source for most South African unis. Its info online is decent, if not 100% complete (
http://www.nrf.ac.za/). Grad student funding is also largely done through the NRF. On the other hand, get an NRF chair and you will be set for life! But this feeds into larger issues of government agenda-setting for research in ways that can make humanities scholars feel somewhat marginalized, as much government money has an explicit development agenda, which lends itself more readily to STEM/social science work.
2 - Educational preparedness of students. You will want to talk convincingly about strategies for dealing with the vast range of skills that students have when they arrive at Wits. So much of secondary ed is in shambles that even very bright students may arrive really, really unprepared to do college-level work. There are some specific efforts at remediation, but still, nationally the completion rate for university students is about 15%. I don't know what time frame that is over, but it is widely acknowledged to be a serious problem. You wouldn't be expected to fix it single-handedly, but I imagine people would be concerned to make sure that you won't freak out at this challenge and quit after a year (as has happened in the past, in the disciplines I'm familiar with).
3 - Relatedly, languages. I don't know what the current status of this debate is, but there is an ongoing discussion of how to incorporate African languages into higher ed, especially since many students do basically all of their secondary education in their home language. For the moment, Wits is still an English-medium school, but it is not outside of the realm of possibility that there will be future serious efforts to incorporate Zulu and/or Sotho through, for example, simultaneous translation of lectures. At the moment, there's not money for it, so no one is trying. But something to have on your radar.