Yes the damper rod on the inside is different from other years, so you cannot use the "special tool" from the other fork seal threads for other years. I widdled down the tip of a piece of wood and shoved it in the top of the damper rod to hold it in place, while I racheted the 7mm hex bolt from the bottom of the fork (with fork in vise grip). No it didn't damage the damper rod at all, and i hammered that mutha up in there good. Here are some pics of the 2004-2009 damper rod for reference. My bike is a 2006. Hope this helps some peeps!
(http://i1337.photobucket.com/albums/o664/Merc110/My%20bikes/damperbolt_zps51f1f171.jpg)
(http://i1337.photobucket.com/albums/o664/Merc110/My%20bikes/damperboltside_zps5ce3654a.jpg)
(http://i1337.photobucket.com/albums/o664/Merc110/My%20bikes/ghettotool_zpsa10c2457.jpg)
(http://i1337.photobucket.com/albums/o664/Merc110/My%20bikes/forkparts_zpsffe67711.jpg)
Thanks for posting. This is incredibly timely as I need to replace the fork seals on my '06 F model as well. I got the seals a few weeks back but I haven't had the time to do the work. Would like to get it done before putting the bike away for the winter.
I'll use the good old Haynes manual as well of course :).