This is how I modify APK's and it works every time for me. Don't forget to sign your APK's when needed.
You only need four files to do this. Not everything that comes with APKMultiTool etc.
a. aapt.exe from the SDK
b. apktool.bat
c. apktool.jar.1.4.2
d. apktool.jar.1.4.3
You will need to pull the framework-res.apk from your phone to your directory.
a. open a command window in the directory you extracted the zip to.
b. type adb pull /system/framework/framework-res.apk
Rename apktool.jar.1.4.2 to apktool.jar
Install the framework.
a. java -jar apktool.jar if framework-res.apk
Decompile framework-res with apktool and apktool.jar (1.4.2)
a. java -jar apktool.jar d framework-res.apk
To recompile the framework you need to change to apktool.jar.1.4.3
Rename apktool.jar to apktool.1.4.2
Rename apktool.jar.1.4.3 to apktool.jar
Recompile the framework.
a. java -jar apktool.jar b framework-res
The *UNSIGNED* framework can be found in ./framework-res/dist/framework-res.apk
If you get "plurals" errors when compiling it means you used the wrong version of apktool.jar
framework-res.apk is the only APK you need to do this for. Everything else can be decompiled and compiled with apktool.jar.1.4.3
Here are the 4 files.
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Thanks to Ghosthunter for the guide.