Install win98 first then Install 2k (don't upgrade to NTFS only thing to remember). Windows install will take care of rest. If 98 install already then there is an option to do a clean install take it and it will take care of the rest.
Assuming that you haven't upgraded to NTFS, you could try to install 98 then do a repair install of 2k. I haven't tried this so it may be really dangerous...
All u need to do is install win9x again, and afterwards pop in your win2k CD and do a repair installation to repair your MBR... that should give you your dual-boot options back...
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