Looks like you deleted those Hidden files in C:\ ;)
I've had this happen. You'll need to boot up with your Windows Server disk and install like Normal (ENTER at first screen, F8 at Second, then you'll be asked if you want to Repair Windows Server 2003, hit R) You'll need to Enter the serial number again - and It'll be like your re-installing Windows (you sort of are) but your data should stay intact.
Uh...Yeah, and don't delete c:\NTLDR that's your Boot Loader and c:\Boot.ini is your Boot file.
As a general rule of thumb, if you can't boot into Windows - but can get past the BIOS - Repairing Windows should fix it.