Guess I'm getting in a little late, but thought I should chime in as well.
Daryl at ACME has access to the suspension dyno's at Kawasaki, which I don't think others here can match. He has also tuned for almost every fast off road rider in America, and has been making the KX500 go fast for as long as a lot of us have been riding. In a nut shell, the guy has forgotten more about tunning a KX than most of us will ever know.
I, too, have spent a lot of time in the desert revalving both my own shocks and forks, but when it was time to race with the big dogs, Daryl got the nod for the go fast tuning.
Here are my thoughts: Daryl does like the lighter springs in the front than I prefer, so you, too, might be happier with the .46 springs. He also likes the rear a little stiffer than I prefer, and like Paul, I run a 5.4. However, leave your oil level at 100mm in the front.
I suspect the solution to your problems are in the clickers. Your fork compression looks pretty good, so start with your fork rebound. Only make one change at a time, and do all of your tuning on a section of trail with which you are familiar and can ride fast. Your shock compression looks to be too little, while your rebound is too much, but this is going to depend a lot upon your riding position. If you ride over the bars, you're probably transfering too much weight to the front of the bike. Drop the shock compression a couple of clicks, and increase the rebound for starters.
If all else fails, call Daryl and give him details on where it does not work, on what type of terrain, and at what speed.
Good Luck
Rick