From what I remember the bearing fit the cases very tightly, and the crank should just slide out of it with a couple raps with a deadblow hammer.. Although sometimes the bearings get heat seized to the crank. It makes for a difficult time when taking it all apart.. After your filing job, try a lil heat and report back if you can find the time. I'm curious to hear your results..
Also, I don't know the extent of your rebuild but pay special attention to the cylinders Nikasil plating. If it's worn either get it replated or have a new sleeve installed, a cast iron one, that can be bored multiple times..
See here:
http://www.thumpertalk.com/forum/archiv ... 42492.html
If you're not a member of Thumpertalk already then I HIGHLY RECOMMEND you join up there! LOADS of information about all makes and models of offroad bikes and motards over there..

Just search there under the Kawasaki section for "crank bearing stuck" or similar..
GB :mrgreen: