As said just loosen the triple-tree bolts and you are set.
I just rolled the bike forward a bit and clamped down on the front brake with the bolts
loose, which in turn put force on the triple-tree , which in turn pushed the fork tubes up thru
the trees. Just make sure when you do this that both sides are equal, as far as you have the same amount on both sides
sticking thru the top tree...
If you ride the thing and like the ride, you could always get a set of tubes made that exact length for a super clean look..