Also is there the potential to see whalesharks at that time in Tofo?
Yes. I was in Paindane in December 2014 (very close to Tofo) and happened across a whale shark on the way to our dive site. The diving around the Tofo area is fantastic, though I've heard there aren't as many Manta Rays as there once were (Manta Reef is, or was, a world class dive site for seeing them). As for transportation, the dive shop associated with Paindane Beach Lodge (there's more than one in the vicinity) has been willing to pick us up from Inhambane airport in the past. If you make reservations, that's something you can negotiate for. I don't know what flights can be chartered into there, though.
Flights can be chartered into the airport at Vilanculos and there's an airstrip on Bazaruto and Benguerra with charter flights. I don't know what's on Bazaruto itself, but have been to Benguerra (a swim away from Bazaruto). We chartered a boat to take us to Benguerra. There is camping and a very upscale resort on the island.
Can't comment on Ponta do Oura or Aliwal Shoals.
Driving the roads in Mozambique can be very hazardous and if you choose to attempt it, I'd strongly suggest driving by day and not at night. Bad drivers combined with poor road conditions can make for a very nerve wracking trip. I would not suggest taking a bus. The bus drivers are insane and I've seen more than one bus get into a head-on collision with a truck along the EN1 (the road connecting the South and North of Mozambique).
I've generally found Mozambique to be otherwise fairly safe from a personal security standpoint. Keep personal belongings secured so they don't get stolen, but I don't hear of much violent crime in the tourist areas.
South African roads are much safer than Mozambique, though there's a lot more violent crime. Be very aware of your surroundings, especially as a female traveling alone. If you have a rented car, keep it locked at all times, even while driving. Watch for suspicious individuals at intersections. Carjackings are common. Use wisdom in where you choose to go at what times of day. Not all of South Africa is this way, but the major cities are, from my experience. I don't want to exaggerate the risk and scare you off. Just be aware of it so you have a good trip. It's not safe like Germany
I'd take 5 weeks. I was there for 3 weeks and it wasn't nearly enough, granted it's home for me so I could've stayed forever. Plan on one destination per week, unless you like to be very busy.
