If your computer boots up fine with the drive letters out of whack, leave it alone as everyone else says.
If there are problems, then you can change the letters around via registry:
1) BACK UP YOUR **** FIRST! Avoid computer lobotomies and do this important step!
REGISTRY:
Select "Computer", click File -> Export. Save that to a flash drive or other removable media.
BOOT.INI:
Also back up your current boot.ini file.
SYSTEM RESTORE:
...and just for ****s and giggles, create a System Restore point as well.
One last thing: restart your computer in some type of mode that allows you to access C:\Windows\System32\config easily (BartPE, WinPE 2.1, Ultimate Boot CD, DOS enviroment, recovery console, etc.). Copy everything in C:\Windows\System32\config to your flash drive of *** saving as well.
2) Restart back in Windows and:
Start -> Run ->
regedit -> click OK.
3) Go to HKEY_LOCAL_MACHINE -> System -> MountedDevices.
Your drive letters are the keys that are labeled "\DosDevices\C:', "\DosDevices\D:", etc.
4) To change the boot drive letter, you need to right-click "\DosDevices\D:", and left-click "Rename." Change it to something unused for now (like "\DosDevices\Q:").
5) Now rename "\DosDevices\D:" to "\DosDevices\C:"
6) Now rename "\DosDevices\Q:" to "\DosDevices\D:"
7) Close the registry.
Check your boot.ini file. It should look something like this:
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /noexecute=optin /fastdetect
If it looks like above, leave it alone. If not, change it to this (this is why I asked you to back up your boot.ini).
9) Restart your computer. If that fixes the problem, great! If not, then boot into the recovery environment you used in Step #1 (BartPE, WinPE 2.0, UBCD, Recovery Console, DOS, etc.) and restore your backup of C:\Windows\System32\Config as well as your copy of boot.ini, restart your computer, and deal with the drive letter madness.