Hey James, this is often a misconception with my riding buddies too. As another member suggests, high speed also has a large affect on ride height in the rear (especially under acceleration). Because of this fact, doesn't it make sense that high speed affects the first part of the travel more?
Oh yeah, this is really going to confuse you!! When I back out of my high speed compression clicker...yes, I do bottom more, but it's not because of that adjuster alone. Because you've softened up the intial part of the travel, it blows through this portion quicker and often "overtakes" the last part of the travel. So, often times, when I back out of the high speed, I'll add a few clicks of low speed!!
Have you ever watched the Nationals on ESPN? Carmichael's mechanic last year, at every race it seemed, always said "because of the choppy bumps, we're going to reduce the high speed compression a bit". Seems like they kept backing off his high speed compression clicker. No wonder his bike looked like a chopper (that and the linkage....)
Also, it's a known fact that shaft speeds on the shock and fork are much higher (although less travel is used) while traversing choppy exit bumps or enter shallow hard terrain braking bumps. High speed can be equated to shock speeds. Landing from big jumps, the shaft speeds are much much slower. Sand is another subject!
So, in a nutshell, it doesn't surprise me that the 2003 Kawasaki's dropped the high speed compression adjuster as there has been a lot of confusion out there. Don't feel bad because the manuals often time don't help the situation.
Bottomline, is feel the effects for yourself. What we tell you in print, won't make sense until you feel it. Suspension tuning sometimes is a black art it seems. First you need something good to work with (springs and valving), then you need to correctly analyze what clickers need to be adjusted and/or if the fork oil height needs to be altered. It's very very easy to go off on a tangent and never find a good setting. It's very important to start with a baseline (the owner's manual or your suspension tuner's recommendation) and work from there.
Much of what I discuss is stuff I have "felt" and after all these years it seems I finally know what clickers need to be adjusted the first time out. I used to fall in the trap of saying "I want my suspension to be plush, so I'm going to back off on the clickers". This might have worked for fire roads, but it sure didn't in motocross!!
We're here to help, but a lot of it is trial and error. Of course, when your trialing and erroring be careful!!