Personally, I'd try to find a cheap, low miles Ninja 250! Read some of the Ninja ride reports. Freaking amazing. Get one under $2k and you won't feel so bad if it breaks so badly you have to abandon it.
That bike is outstanding for any trip like others have said. Mod it up for your specific ride and enjoy!
You DO know, that our summer is thier winter? Bike choice? F800R does the GS challenge <iframe width="560" height="315" src="http://www.youtube.com/embed/DlrkTbbV_bQ" frameborder="0" allowfullscreen></iframe> Luggage protection? Pacsafe locking mesh covers. http://pacsafe.com/www/index.php?_room=3&activity_id=6
There's a Canadian girl from Winnipeg who did some long trips on an F800S, her RRs http://advrider.com/forums/showthread.php?t=805218 http://advrider.com/forums/showthread.php?t=816452 You might find them interesting
Get on whatever you own and go. 70 year old Simon Gandolfi did it on a Honda 125cc pizza delivery bike. http://www.guardian.co.uk/travel/2009/jan/10/south-america-road-trips-bike
When I was stupid and banging around the middle east on roads that were not, filling up with gas that was -- maybe 70 octane... all that shit. I saw every motorcycle that could be pushed or driven -- Honda, Guzzi. Jawa, Enfield. Then I arrived in Kandahar and pulled up to a motel-thing, looking like I had been shat out by a pig. And there was this young couple on exactly the same BMW I had, same color, everything. Except it was somehow pristine and they were gorgeous and perfect like models and... from Toronto. So, make us proud.
If I were to ride South America again, I'd do it on a super moto type bike. (A DR650 with SM tires would be perfect for the trip. Vstroms are popular there too.) Going off road is not a big concern. Soft bags are fine. I used them down there on my last trip. Get a little pelican case or similar for camera/laptop/valuables. The older 650 would be great too. Rebuild your water pump and replace your fuel pump before you leave. I met many guys on 650s that had to replace them on their trip.