Only just noticed this thread, so sorry if I'm a bit late! Running down into Chile from Peru and then into Argentina shouldn't cause you any problems until you start to hit altitude where the weather might get a bit cold. As you're skirting the atacama, rain shouldn't be a major issue, again until you get to the "3 way border area" in the corner of Arg/Chi/Bol where a bit of rain in the mountains might reach you, but as the roads are predominantly tar, the least "technical" route.
Going through Bolivia, high altitudes and bad weather when you're on the dirt roads heading from Potosi via Tupiza to Villazon are the main perils. It is a MUCH shorter route though, and the scenery much nicer than the dull desert highway through northern Chile. Distances between settlements are not great so a bad road is more bearable in short stages. Using the main trade routes means there'll be plenty of passing traffic. There was also a new road being built to the border at Villazon, lovely concrete, but I don't know if it was ever finished. (Anyone else shed some light on this?)
Roads all tar except for stretches between Potosi and Villazon. In an overland truck, La Paz to Potosi: 1 day, Potosi to Tupiza: 1 day, expect long queues at the border but you should make Humuhuaca canyon in a day, or even Salta (but that might be a lot for one day on a small bike)
Good luck, (if you're not already there!)
Simon.
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