My '89 had too much vibration. I had to put buckshot inside the handlebars to make it livable. It's not the first time a manufacturer let part of the bike design be "close enough". If my next KDX is the same way then when I change out crank seals and bearings I will drill 6mm holes in the flywheels to see what happens. If its made worse then I'll have to take it apart and add more metal to that area instead of take it away. I'll post my results.
It vibrated the same after replacing the bearings and although a wobbly crank will cause vibration, I think it is common problem with the KDX since the topic of how to reduce vibration has always been a popular one.
Unless you have a balancer you are taking a crap shoot, the odds of getting it "more balanced" are pretty low. I would get a new fly if you are so sure that is the problem, being a fairly good mechanic, I am sure you already know that as well as the consequences or reducing fly wgt.
Since I started this thread I have devised my own method of crank balancing that I perfected on small engines made for bicycles (since replacement cranks are only $25). You can read about it at www.dragonfly75.com/moto/vibes.html