Sorry, I should clarify... don't delete the Administrator account! Delete the Administrator profile.
You will need to log on as a domain admins person (or local Admins). Then you go to Start and right-click My Computer, and click Properties (System Properties).
On the advanced tab is a button for User Profiles. Delete the one that says <local computer name>\Administrator, or <domain name>\Administrator.
Don't forget to back up whatever Administrator folders you have (icons and such) from this directory:
C:\Documents and Settings\
Then, log an as the administrator and it will create a new Administrator profile in this directory. Next, copy your desktop, favourites, etc. folders to this new Administrator folder, and you should be back to normal.
The only ntuser.dat files you should avoid deleting are in All Users, or Default User. Of course avoid deleting any of them if you can!
This file is essentially the HKEY_CURRENT_USER key from your registry.
As it is already deleted you will not change anything by doing the above. But your Admin profile will be a fresh profile. However, if you have Group Policies in place these will update the dat file as required from initialisation.
As I understand, all you really want is to log in as Administrator and have it the same as before. With the above you will achieve this as far as icons etc., but bear in mind that if you had made any specific registry changes (say, for example, printers added that only the Administrator needs and no one else), then you will need to make these changes again. And if you have any Office shortcuts, or such, then these may be reset as well. A lot of local customization is in the folders though, and not the dat file so you should be fine.
To make sure you back up the right profile, look for the Desktop folder in Docs and Settings\Administrator and make sure your icons are all there. If so, then copy that profile to the new one.
Remember though that in order to have a fresh Administrator profile, without the .0000 and such, you need to dlete all the Administrator profiles (folders) in Docs and Settings, after backing up.
The reason it does this is because when the system does not find the ntuser.DAT for the login, it creates a new folder for Administrator, but finds one already exists, so by default it does Administrator.0000. If you delete the ntuser.dat file from that one, and log in again, you will get Administrator.0001, etc.
This is why you need to delete the profiles to get back to normal. Because unfortunately (I tried this before a long time ago) you can't take an ntuser.dat from one of the other folders and put it in the original. You'll just get .0002 if you try!
Anyway, if you have any more questions before you do it, just let me know.
Will