Really just echoing what others have written.
Capetown is an amazing city. The gay scene was pretty good; there is certainly better, closer. JNB should be nothing more than a pit stop either on your way to CPT or on your way to a safari in Kruger. If you're going to trek all the way to CPT, I would highly recommend you add on a safari, and do it right, i.e., at a high-end place. We stayed at Thornybush Main Lodge and had a fantastic time. There are probably lots of recommendations on flyertalk. I think 2-3 nights of safari is enough. We did 2 -- which meant 4 x 3-4hr game drives (2 per day).
In CPT we stayed at a gay B&B-type place called The Glen. I would recommend it. I also think you'll want a rental car, though note they drive on the opposite side of the road.
Lastly, I also recommend a night or two in the wine country (Cape Winelands) -- Franschoek or Stellenbosch. Stunning scenery - more beautiful than Tuscany, IMHO. We enjoyed our stay at the Franschoek Country House.
In between CPT and the winelands, we did a driving tour toward Cape Point, including the penguin colony at the Boulders near Simons Town.
Good luck!