I went through the same thing while rebuilding my 87 KX250 engine...Still need to assemble it. I'll be posting pics soon.
Anyway, I was able take out ALL my bearings, specially the water pump & governor bearing...that tiny one.
It's a 1/4" x 20 threaded rod, washer and 3/8" socket, slide hammer.
Grind a groove at the end of the rod and make sure the that gap is thicker than the bearing you want to pull out. Not too big because you don't want to weaken the rod. For the smallest bearing I had to make the tip of the rod thin to get under the bearing.
Once you heat the area, insert the rod through the bearing and hook it underneath. Make sure the case does not move. Now keep sliding the hammer and you should see the bearing starting to creep out. It takes practice, but it does work.
The key to making this work is to apply heat. I used MAPP gas (get it at home depot). Heat the area around the bearing. I went around the bearing about 5-10 times. Move the gas around fairly quick and don't stay in one spot otherwise you might warp the case.
I measured about 160 - 170 deg. if I heat the area, going around about 6=7 times. In fact, pulling bearings out, installing main bearings and believe it or not, installing the crank, and putting both crank cases together I did with a temp of about 170 deg. Plus, freezing the bearings.
Good luck!
dinky,