I've got the same issue with my 2000 KDX 200. I find myself hitting neutral a lot when I'm upshifting. I've not found a real good solution other than to shift *firm* (to the point of jerking the lever with my foot). The 1st-2nd throw is long, and I've got a range-of-motion problem with my left ankle anyway. As such, shifting properly is a bit more difficult for me than for most people. I end up lifting my whole leg at the knee in an almost knee-jerk motion.
In the stock location, the lever is almost too high for me to be able to reach with my toe. This is where I have the most missed-shifts. I've rotated the lever 1 tooth down. At that point to get better leverage and the missed shifts start to go away. However, then it's almost too low for me to get my toe under the lever. The end of the lever kind of digs into the side of my boot. I'm also concerned about trapping my foot between the lever and a root/rock/rut/etc, with the lowered lever.
I'll play with it more as I ride it more.
Brandon