From my own conversations at two different borders and from the experiences of a married couple (SA/Brit) I know, you will +not+ get given another 90 days if you exit and enter SA. They will only give you 90 days on your first entry. After that they will only give you 30 days. It is all computerised.
Lesotho is kind of considered part of SA when it comes to carnets and visas (even though it isn't). When I came out of Lesotho they just used my original 90 day SA visa, so my days in LS counted on my SA visa. So doubt that will work either. You might have to try and get an extension in the country, but it is hard work etc
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