It's close. Here is the list of nautical miles distances between the city pairs indicated above:
JFK JNB 6877
LAX SYD 6508
FRA KUL 5377
GRU FRA 5272
There currently are nonstop JFK to JNB flights, but it is unclear whether they existed in the spring of 2001. My guess is that they did exist. However, there were 3 separate flights out of JFK that AR1 teams were placed on, so only one of those was possibly nonstop. There likely were 3 flights to major European hubs like LHR, CDG or FRA that were also used, with connections from there nonstop to Johannesburg.