I believe that if you are on separate tickets then BA will not check baggage through to your final destination. You will have to collect your baggage at ORT/JNB and then check in with your baggage for your onward journey to PE.
We are flying from ABZ to WDH in May on a 2-4-1 ticket, but as the last leg from ORT/JNB to WDH is on a separate ticket with BA/Comair, we will need to collect baggage in JNB and then check in for that leg of the journey.
Very frustrating, but hey ho there's worse things in life.