(1) An Economy class Circle Trip Explorer fare may be upgraded to a higher tiered or First/Business class Circle Trip Explorer fare without fee.
(2) A Business class Circle Trip Explorer fare may be upgraded to a higher tiered or First class Circle Trip Explorer fare without fee.
(3) A First Class Circle Trip Explorer fare may be upgraded to a higher tiered Circle Trip Explorer fare without fee.
(4) Upgrading by sector to Business/First class is not permitted. (5) At any time the Circle Trip Explorer fare may be used as credit towards payment of any higher fare from the point of origin provided the conditions of the higher fare have been met. No fee will apply. Where such credit is towards another Explorer fare, retroactive use will be permitted. Reissued tickets must be endorsed --NONREF/ XXX-- (XXX equals Circle Trip Explorer fare basis code) and the original Non-Refundable amount remains Non-Refundable. If the upgraded ticket is subsequently cancelled, the original fee will apply.
I already see the first mistake in that you are not allowed to stopover in JNB as a first leg of the journey. Not in the same country anyway.
For reissues and upgrades, you can try other OW airlines but they will all point you back to CX for the repricing and reissue.
I'm not sure where this comes from but there is nothing in the circle trip explorer rules limiting stopovers in the country of origin. There is a limit of two stopovers in the continent of origin.
8. PERMITTED STOPOVERS
Note: 1. Maximum two stopovers permitted in the continent of origin.
2. No stopover is permitted in Hong Kong if travel is via HKG – FCO on QF3860/3861.
Any issue would relate to xONEx rules rather than those of the xCIRnn or xONEWCn fares.
There is a rule limiting stopover in the country of origin.
This caused me a real hassle when I last booked an ex AKL LONE4 - the AAgent at the AAround the world desk could not understand that MEL was not in the same country as AKL.
But still, even if this was an xonex this stopover would be proper providing it was the only one in the country of origin outbound. Of course, this is all academic as there is no similar rule for the circle trip explorer.