Don't know if they are interchangeable or not but the part numbers are pretty close so maybe. Best bet would be to call Kawasaki.
99 KX250 Kick Starter Shaft P/N 13066-1099
01 KX125 Kick Starter Shaft P/N 13066-1101
Or you could order the shaft online for $55.47 from
www.oemcycle.com. I bought a clutch cover and gasket from them recently, for abourt 30% less than the local dealer, and was very happy with the transaction.