More that just likely they will align themselves.
The tolerances of the triple trees will do all that alignment for you.
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The Shoulders (wide parts) of the forks are the only part that will fit properly in the trees, but you still have to make sure each side is aligned the same. There is considerable "wiggle room" there. I just put the top of the fork, (or the bottom edge of the cap) right at the top of the upper tree and then its all good