Wow...this looks like a challenge...Good luck!
I have no personal experience, but it looks like the roads are in really good shape in this part of Africa, maybe you can rent a car or hire a driver?
There are trains from Mozambique, if you can get there easier, I don't know...
Link to wikitravel:
http://wikitravel.org/en/Malawi#Get_inHere's what Lonely Planet says:
http://www.lonelyplanet.com/worldguide/mal...here-and-aroundThe Malawian ferry Ilala connects Malawian ports with Metangula and Cóbuč, Mozambique. Train, minibus or your own 4WD are the best ways to get between Malawi and northern Mozambique at Nayuchi. Once in Mozambique, there are twice-weekly trains between Nampula and Cuamba. Crossing other points of the Malawian border will involve a bus, a car or feet. If you're heading for Tete, Mozambique, there are frequent buses between Mwanza and Zóbuč. Other bus routes between Malawi and Mozambique include Nsanje and Villa de Sena, just south of the Zambezi River, and Chiponde and Mandimba.
The only land crossing between Malawi and Tanzania is at the Songwe River bridge north of Kaporo, in the far northwestern tip of Malawi. Buses and minibuses make the run daily. The main crossing point between Malawi and Zambia is about 30km (20mi) east of Chipata, on the main road between Lilongwe and Lusaka. All crossing points on the Malawi border are open roughly from 06:00 to 18:00 .
Let us know what you end up doing.