I have a 2005 KLR. I've ridden it 18,000 miles in the last year, so I'm most interested in how to make the KLR comfortable to ride over long distances -- my best mod has been the Corbin "flat" seat. It allows me to do 400+ mile days in comfort.
I also tried two other seats: the Corbin "dished" seat and a "gel" seat. I disliked both of them because the Corbin dished seat squished sensitive parts of my body and the gel seat was too soft after a few thousand miles.
I've been using the Corbin flat seat for more than 10k miles, and I love it.