Thanks for your help guys. The way that I figured out how to do this is listed below for those who wish to know how I did it.
Open the VS 2010 command prompt as admin.
Open ildasm.exe from the command prompt.
In ildasm.exe, open the exe and do File->Dump (The defaults are OK.)
Copy the dump to a shorter directory and replace the stuff that needs to be replaced, through Notepad++.
After everything has been modified, run the following command in the VS command prompt from the work directory.
ilasm.exe /EXE /RESOURCE=[RES FILENAME].res .\[SAVED IL FILENAME].il
Copy it into place and everything should work well.