I have lowered bikes before, and there's a dandy way that you can put a spacer underneath the damper rod to limit the rebound position of the forks (You have to completely disassemble the forks and then cut the springs to suit). On the lowered bike to the left, I used 4" long pvc pipes in each fork leg, which left almost no suspension travel. And no, I don't ride harleys! It was just a fun project. And a blast to ride...it would scrape so easlity around turns that it forced you to learn how to lean your weight off the bike around corners and ride it upright so you wouldn't scrape so much!
I would suggest a stock set of forks, and if you want to lower the bike a bit, slide them in the trees a bit. You could also find a set of CB550 forks, which will slide into your trees, but are a little shorter. If you are looking to race or corner hard, then I would suggest setting your suspension up a bit more like the racers do.
Most important thing first is to figure out if what you have is stock height or not.