The file is one of the XP registry files. 2 things have happened to your computer. One is the virus, the other is the W2k reinstallation.
Unless the virus has affected the XP system as well, it is quite possible that your XP registry file is actually not corrupt or missing, but it just cannot be loaded.
The problem may well be the w2k reinstallation, when w2k Setup overwrote the boot files. Both w2k and XP use the 3 boot files ntldr, ntdetect.com and boot.ini. When you set up the dual boot, XP Setup put the XP versions of the first 2 files on to C, which have no difficulty in recognising and loading an older OS like w2k. The w2k version of ntldr and ntdetect.com may not be able to load XP, being a newer OS.
Try replacing these 2 files now on your C drive with the XP version first, before attempting a solution with the XP registry.
Boot into w2k. Go to C, and see if you can see the 3 files. These are usually hidden, so if you can't see them, click Tools, Folder Options, view tab, and (1) tick "Show all hidden files and folders", (2) Untick "Hide file extensions for known file types" and (3) Untick "Hide protected operating system files". By doing (3), you also remove the Read-Only attribute of these files, so that you can replace them.
Put XP CD in. Select Perform other tasks, then Browse CD. Go to i386 folder and locate NTLDR and NTDETECT.COM
Copy them to the C drive. Say yes to replacing the existing files. When that's done, remove the XP CD.
Next check the boot.ini file. This file contains the paths to the operating systems on your computer, and determines what the OS selection screen (when you start computer) looks like.
Since you still get the XP option on that screen, the boot.ini file may well be fine.
Under C, double click the boot.ini file. It should open with Notepad. The only line you need to check is the one under [operating systems] which has "Microsoft Windows XP Home (or Professional)" /fastdetect.
The path should be multi(0)disk(0)rdisk(0)partition(n)\WINDOWS="Microsoft Windows XP Home (or Pro)" /fastdetect
where n= the partition number where XP is installed. So if XP is installed on the 2nd partition on the same hard disk, it should be partition(2), and so on. (I assume XP is on the same hard disk as Windows 2000.)
If that's OK, just exit Notepad.
Alternatively, go to the XP partition and find the file WINDOWS\system32\msconfig.exe
Double click it, msconfig will open. Select the boot.ini tab. Click "Check all boot paths". If it returns a message saying it appears all boot.ini lines for MS OS's are OK, then your boot.ini file should be fine.
Then restart the computer and select XP to see if it works. If it still returns the error message about the registry file, post back. There are MS articles which deal with it.