Back up every apk that you want to replace by renaming it with a .bak. Place modified apk in the root of /system, and change permissions to rw-r-r and Move it to the app or framework folder. Replacing framework is very dangerous, but I have found that a factory reset will allow you to replace it with the original, if something goes wrong.
I recommend doing this process slowly. start with two apk's, then reboot, check to see if they work. The other way to get framework to work, is to pull a COPY of your original, and inject the images into the res folders. Do not try to extract framework, then repack, it will boot loop.
Use these at your own risk, as I am not responsible for your actions.
Special thanks to BobCatRom in the S4 forums for sharing some of his images.. Click the thanks button over there also
Also, I used some of the framework images from the Cobalt theme, those guys/gals do amazing work. Be sure to thank them also