Hmm.... Installing ME or a 9x series windows after an NT based system (nt4/2000/xp) will certainly blow away the NT MBR, and skip the NTLDR.
Now, what you should be able to do is this....
1) enable BIOS virus protection
2) install win 9x.
3) reject the new MBR (bios virus protection backs up your MBR, so rejecting the change reverts you back to your previous MBR)
4) reset BIOS to normal.
5) cross fingers and boot.
If this doesn't work, you should be able to boot from the 2000 install CD (or boot disk set, whichever you used) and do a REPAIR (rather than re-install). When it comes up, it should realize that the MBR has been trashed and set it back to it's defaults. You may need to edit your BOOT.INI though. (Hmm... why not back that up to a floppy before you do anything, that way, you know what it's like, in case the repair then skips letting you dual boot.) The BOOT.INI file controls the options you see for loading when first booting.
