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If 2K Boots from CD, why not do a full format of your c:\ drive. This should write over the boot sector.
Can't you even boot from a Win9x startup disc and FDisk?
Althernativley, if you have another hard drive, set that as the Primary Master and the other as a Slave, use a CD/disk to boot, and wipe the Secondary (low level) hard drive which would be your faulty one.
HTH.
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