Switch Cmd and Control keys for one app only

I use a mac at work and a home. However, at work I need to log into a Windows virtual machine (using either CoRD or MS RDC) several times each day to do some work. Switching between using control instead of command for common keyboard shortcuts is driving me mad, so I was hoping there was a way to switch these keys only when I am in Windows. That way I wouldn't have to fight my muscle memory for tasks such as cut, copy and paste. (Permanently switching my mac to use a Windows layout is not a solution btw. I like my mac keyboard layout)

I have looked at Ukulele, but it doesn't allow rearranging of modifier keys.

It's a common issue and it looks like it was answered on superuser side of this web site - Assuming you are happy with a solution for Remote Desktop, this looks to be a duplicate of https://superuser.com/q/263647/76395

Have you had a chance to see if that program will help remap the keys as desired?