Cathay would be the obvious people to work with since they are the next 5 flights on your route. Call them on +66 2 263 0606 and see what they suggest.

But they only seem to have an office at the new airport...

Your proposed routing looks fine to me. The difficulty with the JNB-MRU-JNB may be that flights are not yet loaded into the reservations systems for the dates you want. Once they are it shouldn't be a problem. Remember that you can always get segments issued open-dated if that helps.

But also - $30 is par for the course these days. BA and QF would charge you that at least if you managed to deal directly with them. It does raise the question of what exactly the $125 is for, but at the end of the day it's irrelevant if no-one will actually do any work without an additional fee.

Which airline do you have status in as a result of your trip so far? Particularly if it's AA then you could call the AA RTW desk and get them to set up a PNR for the reissue for you. But this is likely to cost you more than the $30 that the TA wants...