Thank you for contacting FixYa with your inquiry.
The first thing we need to do is eliminate the possibility that the shift lever is not interfering with anything limiting it's travel into the top three gear positions. It's possible that the lever is bent or has been incorrectly re-installed on the wrong spline position.
That being said, we more than likely have a problem with a bent shifting fork, a pall, or a shift rail, maybe even a broken gear.. There is also a good possibility the engine has been previously disassembled and not had parts replaced and the engine did not get re-assembled correctly. You will have to remove the engine and split the case to inspect the shafts, shifting forks, spacers, and shifting drum to correct the problem. This link will take you to the complete shop repair manual for this bike. Check the section 4 beginning on page 36-37.
http://www.scribd.com/doc/44875530/20355873-1998-03-KTM-60-65SX-Service-Manual
You may have to make some holding parts and/or rent some pullers but it's not to bad of a project. A good KTM Shop can always fix the problem but it's expensive. This is a great little bike. I'm sorry it's having problems.
Thanks again for contacting FixYa.
TF
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