Groatse,
Loads of South African owners of LSA/Experimental aircraft fly their planes all over Africa.
I think it is only Zambia that has a problem with Non Type Certified aircraft.
You should direct this question to the South African aviation forum
AvCom - Your Aviation Community , there will be hundreds of helpful people who will give you good advice on that forum.
If you could be more specific about your route and destination that would help as well.
Most African countries do require an overflight or landing clearance, a general rule of thumb is that if they have granted the clearance, (there are company's that will do all the clearances for you for a fee) they are accepting the aircraft, normally certified or non type certified.
Good luck.
Max.