Does the '06 come with the adjustable preload caps on the fork. If not you could buy them to increase the preload for running fully loaded and to get the sag numbers a little better, also you can just add shims inside the caps to do the same. Really it is simple.
If you are short legged like I am you could shorten the springs which will automatically stiffen them and lower the bike at the same time but then you need to put a limiter internally. Again this is not real complex, a good shop can help you or do it yourself. Changing the preload is explained in the WP manual for front suspenion that comes with the bike. If you decide to shorten the fork, use a lowering link on the rear shock.
I have done all this to my '02 640 adventure and it does not wreck the handling like some say, in fact on gravel you will fly especially if you add a Scotts steering stabilizer. That is a must in my book anyway. I stuck about a thousand dollars in my suspension but I lowered the bike 4 inches, got the caps and the steering stabilizer and had the front forks revalved.
If you e-mail Sommer KTM in Austria they will tell you what to do to make the bike right. They are supporting a large number of riders all around the world. I am on the Adventure rider forum as bmwktmbill. If you post there you will also get plenty of advice.
Once you get the bike load it up with gas and gear and set the sag front and rear. Ride the bike and try it. Don't take someone else's advice. The front end moves quite a bit even when shortened but if it isn't bottoming it is working right. Try it first you might like it.
My 2 cents.