The Transalp is a Honda, but now 10 years old, so it would be imperative to find a good clean example and go through it thoroughly before leaving.
Modern single cylinder bikes to consider would be the BMW F650 (either 99 Funduro or 00 GS), the Honda XR650L (or new XR650R with a Baja Designs kit), the Kawasaki KLR650, or the KTM Adventure.
For twins, you are probably limited to the Transalp or a BMW R80G/S or R100GS.
If you are leaning toward a dirt-oriented single, I advise you read the following article on the Thumper Page:
It compares the KTM with the KLR, XR, and F650.
It is possible to ride the entire route you mention on tarmac, with the exception of parts of Ecuador (and the Darien obviously). As such, you could use a street bike, if that suits your fancy.
I would be happy to discuss the route with you further; I am planning a similar trip, albeit in stages, and am in SoCal.
bjorn_edstrom@hotmail. com (space is there to foil spammers -- delete it to email me)