I also forgot to mention before I did the LS400 brake swap, I took my caliper bracket bolts out & put lock washers on them. That eliminated the clunk.

 

Having this same problem. It only happens under 5 mph when coming to a complete stop. It's weird because I've had the problem off and on since owning the car a year ago. It's all connected to the brakes, booster, suspension, transmission, wheel hub and wheel speed sensors. Any those things can cause the "braking 2 step" as I call it at low speed braking. The problem can be just as simple as air in the braking system, bad alignment, suspension parts, rings in the wheel hub bad, bad connection with wheel speed sensor ( dirt, hub ring, or cut wire ). Out of all things I mentioned and was fixed and/or replaced...It was the hubs.

 

Check your brake caliper bracket bolts.