First boot into 98 and make a windows Startup disk next delete these files from your c drive boot.ini, ntldr, ntdetect.comThen reboot with the startup disk type this at the prompt
sys c:
and hit enter
then run fdisk to remove your non dos partition (if u formatted w /NTFS)create a new partition and format it with fat 32
if u formatted your 2000 with FAT32 just format the drive
note you have to enable your system to see hidden files and system files to do this