Are the springs shorter than stock? If so then two possibilities:

1) You've changed the geometry enough that the sway bar is whacking something

2) If the spring is short enough then it might be unseating slightly when the strut extends over a bump. When it compresses afterwards it reseats with a clunk. this is very common with drops of more than 1"

If not then I would look again at the fork and the brake line ring that goes around the shock. They can appear properly seated when they are not.

Also, and I know this sounds stupid but its happened to me. Are you absolutely sure that your lug nuts are torqued? Loose lugs can sometimes appear like all sorts of other suspension maladies.

I like Mike's idea about exhaust components. Do you have aftermarket exhaust or headers? I would check anything that's not stock.