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There is a jumper on two of the three prongs from the CMOS. Do I put it on prongs two and three and then put the tower back together or do I just put the jumper on and then quickly remove it and put it back on prongs one and two?
Choice # 2 ... Put it on then remove it and put it back.
This will clear the CMOS but Windows ME doesn't use NTLDR so there is some confusion about your original problem. Have you tried to upgrade to Windows XP or 2000??
What you need to do is get a Windows 98 startup disk.. Boot to drive A the type DIR C: and hit enter.
If you see files then you still have a fat32 partition and we can try to help you make it bootable.
If you get an Ivalid disk error then you either have a NTFS partition (which Windows 98 cannot read) or something else is wrong with your hard drive.