OP, I have AA award miles on QR from JNB>DOH>DFW in business but have to fly on a separate ticket on Airlink from Windhoek earlier that day. I am not optimistic that Airlink in WDH will interline and through check my bags on to QR back to the US. But I will try in WDH but it is a very small airport and agents may not know how or be willing to do that for me.
Fortunately I have a 4+ hour transit time in JNB which will allow sufficient time to get through immigration and security if I indeed need to reclaim and recheck my bags in JNB.
Not my first rodeo to transit in JNB and yes, it can be very slow. I arrive around 9:10 am so will likely experience a lot of long haul flights arriving then.
Good luck with your tickets but if you an manage to get a later Airlink flight out of JNB I would try for that.