Just modify the [Colors] section in Rules.ini. If you also want the new colors to show correctly in the multiplayer game screen, this tutorial seems to cover it:
http://www.tiberiumweb.com/forums/index.php?showtopic=52And as I've already told you, just download Hyper's no-cd version of his WaveClass fix, replace your TFD Game.exe with it and edit it.