We toured through Botswanna and Namibia in June 1999. Entered Botswanna from Victoria Falls, across to Swapkomund on the coast and then south to Windhoek.
No problems, except for one random Police road block in the middle of the Namib desert, ostensibly a vehicle check, which was more amusing than a problem. The obviously inexperienced officer took one (almost new) bike for a ride to 'check the brakes', but returned a few minutes later and let us go. It was an ego thing.
Especially good vibes in Botswanna. We left our 1100GS in Maun for three days and took a plane ride to the Kwando resort in the middle of the Okavango delta. Expensive but worth it, a real highlight of the trip.