Grab a bootdisk from
www.bootdisk.com first and get to the dos prompt.
Get to the C:\ prompt. Then type attrib -s -h -r msdos.sys and hit Enter to remove the system, hidden, and read-only attributes for this file.
Now type edit msdos.sys and hit Enter. In the resulting window, look for the section titled [Paths] and see if it has the lines WinDir=C:\Windows and WinBootDir=C:\Windows and make sure that the path after the '=' sign corresponds with wherever Windows is installed. (you will have to remember what you renamed the drive letter to)
If those lines are not present add them manually as follows:
[Paths]
WinDir=C:\Windows
WinBootDir=C:\Windows
After making the necessary corrections, save the file and exit the editor. Now reset the correct attributes for the file by typing attrib +s +h +r msdos.sys and hit Enter. Now reboot and see if it now boots correctly into Windows.
If this works and you can boot into windows -
Immediately go into Disk Manager and correct the boot drive letter!