To add to what George has suggested, altho it's some time since I visited Marakele, there is (or was) a good supermarket - I think it's a Pick 'n Pay? - in Thabazimbi, just a few kilometers before your reach the park entrance. That's if you're taking the R516 to the R510. I am not familiar with the mall at Lephalale. However, if you're passing thru Alldays, you can get excellent meat at a shop at the petrol station that is on the R572, just off the R521.
As for shopping in Mussina, I FAR preferred the Shoprite, which is in a mall on your left as you enter Mussina from the west. I found it better than either of the town's two Spars. As well, if you need to top up petrol, so far as I know the only petrol station on the main route thru Mussina is the Shell at the eastern end of the town.
Also, if you plan to enter at Pafuri gate, there is (or was) a detour at Masisi along the R525 (around a washed out bridge) that is (or was) not at all well marked when you're approaching from the west. If you can't find it, just ask and you'll be directed to the entrance gate for the detour.
Enjoy your trip! Mapungubwe is one of my favourite SANParks
