I just went through the same issue with a basket case bike I bought "cheap" and the following should give you a good idea of cost.
crank rebuild parts and labor $160 using Hotrods kit
crank bearings $90
gasket set $120
Countershaft seal $12
Misc unknown $50
Total ~ $400
You are assured to find a few more items that will need help along the way.
FYI there is a 1998 250 crankshaft on ebay for $75.
Good luck.
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