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sorry, I meant triple trees, not the fork tubes. I know I'll need to pull the top tree, but does the stem bolt just slide out of the bottom of the head tube or does it need to be pressed out?
I believe that you need to remove the forks, than the stem nut (loosen to finger tight before pulling the wheel & forks) than pop off the top tree than remove the cerated nut and washer to remove the stem. A parts manual is a really good thing available here for a 2006 bagger which is near the same thing.
As stated above, everything should come apart no problem. The bottom bearing should be the only one that needs to be pressed off. Although you can sometimes get away with heating/cooling it and tapping underneath with a punch - that is what I did since I don't have a press. For re-installing new bearings I froze the bottom triple tree to shrink or condense it, and then heated the bearing up to loosen it/make it bigger. This was just enough to be able to reintsall the bearing on their without a press.