I don't think there is anything specific to the 06...could be wrong. But, in general:
1) You'll want to know if the doohickey has been done.
2) Any other changes...lowered? Raised?
The rest is basic stuff for buying any used bike. Me? If it's dirty, I don't buy it (I figure the least someone can do is clean it). Check the chain...you can tell a lot about how someone maintains their bike by the chain. Was it ever dropped? As Paper pointed out a while back, if you can, look at the garage/house. This will also give you some insight into how the PO takes care of their shit.
Other than that...I mean, the KLR ain't a real complicated machine. Give it a good look over. If anything seems weird, including the seller, there are more fish in the sea. My .02.
"In a car you're always in a compartment, and because you're used to it you don't realize that through that car window everything you see is just more TV." R. Pirsig
Soon, we ride.
AKA JD Mader or you can call me "Dan" just not early for dinner.
Click my handle for a link to my homepage/blog...which has nothing to do with MCs. Free literature and music! Viva La Revolucion!
2008 KLR 650
RIP DM - Soon, we ride.