Hi Stuart,
I think the 690 is the best bike for it (apart from the 640 Adventure perhaps). I bought one 1,5 years ago and love it. 15.000 km only so far (mostly 2-3000 km trips in Europe) and I have had no issues. I have done trips alone and two-up (my girlfriend loves the bike, too) and I have done motocross trainings and the Enduromania (amateur offroad competition) with it. It is great offroad (use the offroad engine mapping and perhaps a smaller front sprocket) and huge fun onroad as it is both light and powerful and has very good suspension. Other singles I have ridden (BMW F650, Tenere, Suzuki DR) feel sluggish and antiquated in comparison. It don't like it for fast motorway riding though: it is fast and stable enough and does not vibrate much, but it is tiring due to the lack of wind protection, so usually I do only about 100-120 km/h for a more relaxing ride.
Regarding your questions:
Reliability: Apparently much better than the old LC4s (which are better than their reputation). The German Motorrad magazine has done a 50000 km test (with the Duke, which has the same engine) and was impressed with it:
Dauertest-Abschlussbilanz: KTM 690 SM - Motorrad-Dauertests - MOTORRAD online As I said, I have had no issues.
Servicing: Easy to work on (much easier than the new 660 Tenere as a friend of mine who owns one says). You need 10W50 or 10W60 oil though. The 2008-2009 models have a service interval of 5000 km, the 2010 model one of 7500 km and the 2012 model one of 10000 km. So if you are happy to carry 2 litres of oil you have a 20 k range with the newest model (and I suppose the other models will also survive a 10 k interval).
Modifications: I bought a new seat (Kahedo is comfortable and I strongly recommend it), engine and radiator guards, small screen and a luggage rack (all Touratech). Even if you use soft luggage I would recommend a rack to support the tank (there is no subframe). The one from Touratech is probably heavier that the one from KTM, but seems much stronger. What still bothers me is the extremely hot standard exhaust (don't want to shell out 500 Euros for an aftermarket one though), the lack of a centre stand and the small tank. The tank is big enough for Europe due to the good fuel efficiency (3.6 l/100 km on my last 2500 trip, 0.5 l less than the new 660 Tenere on the same trip), but for Africa? Rather than buying an expensive tank I would consider using fuel bladders or canisters. Btw, there is also a bad fuel engine mapping which may be useful in Africa. Some people recommend replacing the original tank bolts with stronger ones and protecting the radiator better. Check
RTW KTM 690 Enduro - ADVrider , there is a lot of useful advice.
My general advice would be to keep it as light as possible. As with any bike of course, but this one benefits particularly from it as it is very light itself and you will want to preserve the offorad capability. Try to move as much weight forward as possible (especially the liquids and the tools), also because the fuel tank is at the rear.
Hope this helps!