Starting from WPS 6.1 you can create a Theme or Skin in separate .war file and install it on portal. You dont have to modify the wps.war any more. I followed the Infocenter Instructions for Creating a new theme and skin to create MyTheme.war and MySkin.war along with my own version of DeployTheme.xml that i can use to deploy both MyTheme.war and MySkin.war. Attaching those files below
First install MyTheme.war and MySkin.war as enterprise applications from the WAS Admin Console and then execute the DeployTheme.xml as xmlaccess script.
