I haven't ridden a 650 Dakar on the highway, but I can give you this experience.
I rode a 1200 GS Adventure a few weeks ago on a group demo ride. It was a 45 min ride with a good amount of highway and for a demo group we really opened it up. Probably hit close to 150 km/hr. The bike behind me was a f650 and he was taking up the rear. I couldn't believe how well he kept up. He was a small guy, but he was able to keep within striking distance the whole time. He couldn't accellerate as quickly in the higher gears, but he sure didn't have any big issues.
I also had a long conversation with a local guy who has traveled extensively in South America on his Dakar. He actually prefers the 650 over the 1200 for speed as it is, in his words, more nimble.
As far as the other questions, I think Doug hit it all. The only things I would add right now (other than cargo/saddlebags type of stuff) is a windscreen. If you are hitting sections of tarmac for any extent, there is nothing as pleasant as a well designed and setup windscreen. And also the seating surface. Nothing is worse than a poorly designed seat. Spend the money and go with what works - be it custom or not. Your but will thank you for it.
/ -- \ Pete Hartl - VE6PGH - 0VRLAND
EXPEDITION = (Encounters + Adventures + Experiences) x YOU