I don't like the Trailwings either, but they'll get you across Canada just fine. Then definitely replace them with something better suited to the roads (and lack thereof) in Africa, maybe TKC-80's.
No one has mentioned lights. Even if you don't plan to, on a trip that long you'll probably ride at night some. The wee's headlights are good, but it's always good to have more, especially when you're in the middle of nowhere. Auxiliary lights also help you be seen, day or night. 35W halogen or some of the new 10W led lights will put light on the road and leave you enough power to run the heated grips.
+1 on Eastern Beaver electrical products -- Jim has high quality,
Strom-specific plug-and-play kits for lights, grips, power sockets (you'll probably want those too), and a nice fusebox. If you're going to be on particularly rough terrain, you might want to check out the ABS switching adapter.
Givi or Trax would be fine for a topbox, but I would prefer something tougher for sidecases. I still use a pair of Caribou/Pelican 1550's that survived the crash that totaled my last wee. This computer was in the case underneath the bike as it slid down the highway on its side, and the case, though even uglier than it was before, is still watertight. I'm not really a fan of side-opening cases, but the lid lanyards and elastic retention straps added by Caribou, along with a set of liner bags, make them tolerable. They're also cheaper than almost anything else of comparable volume. Did I mention they're indestructible?
If top loading is a must, Happy Trails seem to be the best aluminum case systems under $1000. The HT racks even have a place to mount a tool tube.
Otherwise I agree with all the stuff on your list, although the fender extenders are unnecessary with the Motech skidplates mounted.
As others have mentioned, fork upgrades and fork braces are a good idea. Considering the loads you likely will be carrying, a shock upgrade is in order as well, especially if either of you weighs more than about 180lbs.
Offroad-style footpegs -- better traction, broader base for more comfort.