Converting a land segment to an air segment
 

I have recently ticketed:

SFO-ORD,
ORD-PVG,
ICN-HKG-DEL,
DEL-HGK-JNB-WDH,
JNB-MRU,
MRU-JNB,
CPT-LHR-CAI,
JMK-LGW-KEF
KEF-LGW
LHR-ORD

I messed up and did not request an air segment from JNB-CPT, but requested a land segment.

How easy or how hard would it be to add a JNB-CPT air segment...or should I just keep this as is and buy separately?

I am okay in the number of African segments...based on the new rules land or air segments count the same.

Simply, you need to reissue your ticket at cost of 125 USD and applicable tax and surcharge.
If cost of separate ticket is cheper than 125 USD,
the answer is .....

If you are certain of your dates and times you would definitely get a ticket on a LCC for less than $125 (which is approx ZAR900). Fares are available for R300 (approx USD40). But it won't be as flexible as your ONE ticket and it certainly won't be in J (assuming you are on a DONE or AONE).

I assume the answer is the same if I cancel JNB-WDH and change it to WDH-JNB...?

Yes, in that it requires a reissue. No, in that I'm not aware of any LCC's offering cheap fares on this route - the cheapest fares are almost $200 one way. (I stand to be corrected on this since Kulula claims to fly to Windhoek but I can't find a timetable for that route.)