Here I am just going to explain how to use NinjaMorph as per request from those that have the app.
NinjaMorph was made so that we could more easily make changes to the system apks and jar files from our phones without needing to apply a packaged theme or hook our phones up to the computer.
In order to use NinjaMorph you will need Busybox installed, cp properly symlinked, and at least 20mb of space of your SD card.
When you first open the app you will see three buttons at the bottom.
The first is "New Project", which is the one your going to start with.
Select "New Project" and navigate to an apk or .jar file of your choice, excluding apps that need to be signed like Market apps.
A good example would be for you to go to "System" > "framework" > "framework-res.apk"
The app will then extract the contents of the apk, as well as making a backup of it on your sdcard "/sdcard/AndroidThemes/backup/"
After its done it will ask you to pick a file to change, navigate to "res" > then a drawable folder with images in it.
Once there you should see all the images there in that folder, select one and it will ask you to pick one to replace it with, NinjaMorph will rename the file you pick to replace it to the appropriate name.
After that just keep changing things until you've done everything you'd like to do.
If you have an existing project you can use the "existing Project" button to continue where you left off.
If your done with your project and you want to apply the changes, Choose the "Finish Project" button and select which project you want to finish, NinjaMorph will do its thing and thats it.
Note that after making some changes you may need to reboot to see the changes made.
Anymore questions, ask away.