Fixed NTLDR error by recovering partition but boots wrong

[SandraDee]

I did a clean install of Windows 2000 with NTFS on one partition. I was getting the "NTLDR is missing, Press any key to restart" after Windows updating, installing SP4 and getting blue screens. The C drive was showing files with weird characters and 10 mb size hd. My hard drive is 80 gigs. Finally, I tried TestDisk and it showed my original partition was deleted. So I undelete it and windows and all my data is back on the C drive. Though when I boot my computer I get this:

Starting Windows 98...

You are using automatically generated configuration
files.
Your original configuration files have been renamed
Config.upg and Autoexec.upg and are located in the
C:\MSDOS7 Directory.

Then it goes to the C prompt.

I followed Microsoft's resolution to remove the lines from the Autoexec.bat which worked, but it still says "Starting Windows 98..." and goes to the C:\ prompt.

However, it says the file system is FAT32. I almost have sworn I used NTFS. I did have Win 98, but used Western Digital's software to format and partition the drive. I think I read somewhere that I should use win2k disk in addition to that as it won't completely remove everything. Is this why it wants to start with Windows 98?

I copied ntldr, ntdetect.com to the c drive and still don't work. Went to recovery console to repair and doesn't work. RC actually showed there is only one Windows installation. Created a boot disk and my computer hanged after "ROOT FAT." Chkdsk /p /r fixed some errors, but I think it said there wasn't enough space to recover all of it. The boot.ini is fine.

How can I get it to boot to Windows 2000? I don't know where this Windows 98 message is coming from.

[Darthgary]

After you copy the NT Load Directory everything should work.

Swallow hard and use Fdisk.

[SandraDee]

Where is this located on the Win2k disk or what files are these?