EDIT: Further explanation...
The com.apple.mobilesafari just tells winterboard what the name of the package that it's changing the icon for is called, not the location. You just have to look up the actual location of the app and change the icons. This is how you do any apps. The app store ones are more difficult because they are all hashed names and you have to go by trial and error to find them. If it was com.apple.springboard then it's in the folder you mentioned.
Yea.... I wasn't talking about using winterboard. I was saying taking icons OUT of a winterboard theme...
Also, /Applications/ is a symb link to /private/var/stash/Applicatoins.#####/ because the things after that . are different for everyone. So /Applications/MobileSafari.app does work and will work for everyone.