Hi CMan,
I do trips up to Moz on a regular basis mainly for Diving off Barra so can give you a few tips about Moz itself, Never had to travel from CT though so can't help you with that, But should imagine that the roads are better going through JHB rather than the Transkei, also just checked my distance charts, CT - Maputo via JHB +/- 1900km & CT - Maputo via PE +/- 2300km
Here some other tips from my experiences in Moz, use them or don't they may help somebody else??!!
If you go through Ressano Garcia border post (Route from JHB) expect some "harassment" and we have had to pay bribe money before or for somebody to help, things can get confusing at the border post lots of queues, but you'll survive. for the last two years I've been taking advantage of the newish Goba border post (From Kzn - Swazi - Moz), normally very quiet and they have computers!! once through the roads are now in fair to good state, last year only 100km patch just after Xai Xai otherwise very smooth going! Just one thing don't drive through the night did it once 6 years ago and never again trucks and buses drive in the middle of the road and often had to drive half off the road to avoid an accident. lots of good accommodation in and around Maputo, last two years been staying in Maputo, previously stayed at Casa Lisa which is also a comfortable, clean stay over. From Maputo it can take about 6 hours to Pandane. Watch out for cops, every time you see the 80km per Hour sign SLOW DOWN to the speed limit and follow the speed limit until you through the town!!
Fuel up before entering Moz, last time I was there fuel was more expensive than SA.
Shop around for fuel, different prices at every fuel station a good place to stop is in Xai Xai more or less half way and a few fuel stations. Trust me you don't want to get stuck in a small town with no fuel!!!! once at Pandane a trip into Inhabane is worth it to fuel up. Oh yes and take toilet paper with (white gold) if nature calls better to squat next to the road than most of the toilets on route, especially if the Women are with.
Hey now I'm itching to go, I'm sure you going to have a blast, If you doing some Scuba Diving or even snorkeling off the boat you must get in the water at Manta Reef, Mind Blowing.
I hope this helps?