Stand up on the pegs, slow down a bit, hit it as much "head on" as you can.
In short, treat it as if you were riding off-road. It's what a KLR is made for.
On a side note, I was coming up from Baja this weekend. I hit a stretch of highway between Ensenada and Tijuana that is ripped up; it's an earthquake zone and the San Andreas Fault runs right through it. The area is constantly torn up.
I always smile and rip over it at 65 MPH as if I was riding the Dakkar.
You'd be surprised what this bike will do if you let it.