If the RMA is going to take a bit and they won't do a cross-ship I would recommend just popping out the old drive, setting bios to boot to your remaining drive, and reinstalling Windows on the new drive. Choose NOT to format the disk during setup so your data remains intact. When the new drive arrives, simply add it as a secondary.
If that sounds like a hassle, wait till you hear the alternative:
What is required to boot:
A drive formatted by an NT based OS so that it has the proper boot sector.
NTLDR
Boot.ini with the appropriate arc path
NTDETECT.COM
Right now your bootsector and the above files are on C: and this in turn transfers to your OS (\windows folder) on D:.
Remove and replace...
If they cross ship, you can
remove and replace the drive, kick off windows setup long enough to partiton and format the new drive with NTFS, then drop the above mentioned files on and you'll be good to go.
If they don't cross ship and you gotta take C: out for a while...
If you simply remove your C: drive, you can get booting again by dropping the above files on the D: drive and editing your boot.ini. I'm *guessing* you'll need to go from:
multi(0)disk(0)rdisk(1)partition(1) (First partition on 2nd disk)
to:
multi(0)disk(0)rdisk(0)partition(1) (First partition on 1st disk)
Now this will get you booting again but you'll have a rather serious problem. Your drive letter will have shifted. Everything that was previously running on D: is now shifted down to C:. You will first notice this because when you try to logon it will drop back to the logon screen again. Winlogon is trying to start
D:\windows\system32\userinit.exe but it is now loaded on the
C:\ drive. If you have another computer on your lan you can fix this by editing your registry remotely while it's at the logon screen. If not, you're gonna need to fix this beforehand. Remove the path from the userinit value located in the following key so that you are just left with "userinit.exe,":
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon
You can now logon but sh1t will be all frankensteiny (tm) because every other reference to D:\ in the registry is wrong. You're gonna need this for starters:
http://support.microsoft.com/default.aspx?scid=kb;en-us;223188
Fix all that crap, or limp along until the replacement drive arrives and then follow the "remove and replace" instructions above.