SA is a very good place to go to do a license and then convert it. I know several people who have gone out there and at the same time done distance learning for their JAA ATPL's in parallel with their SA CPL Ground Schooling. The syllabus and system is closely allied to the JAA syllabus so there is a great deal of commonality, which makes conversion a great deal more straightforward.
Like everywhere, however there are good and bad FTO's. Here are some I have heard good things about: 43 Air School, Progress Flight Academy and Central Flying Academy. There was an outfit in Jo'burg at Grand Central who gave the industry a bad name when they were training and had JAA umbrella approvals through another organisation. I understand they are no longer trading which is a good thing. As far as IR training is concerned the SA IR is 'procedurally' based like our own and the test is very similar to our own, possibly a little more stringent in some areas, unlike the FAA IR which is geared much around their own systems and has little or no procedural work.
Hope this is of some use to you. E S