If you only want to shorten it an inch or so, you can cut that amount off the top of the fork springs. Recall, the shorter a spring of a given coil is, the stiffer it gets. If you ever need that height back, you can cut a spacer out of 3/4" PVC to put at the top of the spring. You can only take so much out before you run the risk of bottoming out the upper tubes. Technically, you CAN shorten the upper tubes, but there's not a whole lot of space to play with between the front wheel and the lower tree.
If you plan to raise the fork tubes in the trees, you will need to get a set of dogbone risers to keep the handlebars away from the forks that are now poking up through the top tree. The other option, of course, is to run clipons, but not everybody likes those.