You could also use GuiKitty to extract the theme and dig through the result to find the relevant resources for the app. Then go into the resources for the app (right click -> show contents -> contents -> resources -> look around in what you can find) and replace the themed resources with the installed ones.
Just remember that your custom app changes will be overridden by any running ShapeShifter themes unless you exclude that app in the shapeshifter preference pane.
Oh yeah, a note about finding relevant resources extracted with guikitty - they aren't arranged by app, they're all kind of thrown together. What makes things easier is to have the theme running in themepark, and then go through the extracted resources with Preview to look for things similar elements.