[Samsung Galaxy Nexus] EnixLHQ:
Alright, everyone. I've figured out how to pull this off. All links I'm providing are from posts already in this thread and are to put everything into one place.

This is a step by step process.

Just be sure we're on the same page, delete any folders and downloads you've already tried. Also, go into your C:\Users\username\ folder and DELETE THE APKTOOL folder! This will ensure a virgin install and should minimize any issues.

Step 1: Download he_stheone64's version of APK Manager here: http://www.multiupload.com/JCTFOH7DQ6

Step 2: Extract the contents of this zip into a new folder (named whatever you want, but with NO SPACES, IE: apk_manager) in your C:\Windows directory. (Why Windows? I'll explain later.)

Step 3: Download he_stheone64's zipalign batch here: http://www.multiupload.com/IAFR5U6OJ4

Step 4: Extract this into it's own folder anywhere you like. For simplicity, put it into your apk manager folder.

Step 5: Download he_stheone64's template images and xml files here: http://www.multiupload.com/LFFT3Z4P02

Step 6: Extract this into it's own folder anywhere you like. Name it in a way you know you will be copying files from here eventually.

Step 7: Launch the Script.bat file.

Note: If you like pulling your SystemUI.apk and Framework-res.apk files in other ways than ADB, you can skip to step 8.

Step 8: Choose option 0 and pull your SystemUI.apk. It will be located at \system\app\SystemUI.apk and you can name it whatever you like when prompted.

Step 9: Choose option 0 again and extract the framework-res.apk. It will be located at \system\framework\framework-res.apk and you can name it whatever you want when prompted.

Step 10: These files will now be in your place-apk-here-for-modding folder. If you skipped to this step, well then PLACE these files in this folder.

Step 11: Choose option 22 and select framework-res.apk (or whatever you named it) as your current project.

Step 12: Choose option 9 and decompile framework-res.apk.

Note: The astute of you will notice that when this step is working a new folder will be created under C:\Users\username\ called apktool and inside it will be a framework folder with a file called 1.apk. THIS is the reason we've been failing. I'll explain later.

Step 13: Choose option 22 and select SystemUI.apk (or whatever you named it) as your current project.

Step 14: Choose option 9 and decompile SystemUi.apk.

Step 15: Copy the contents res folder from he_stheone64's source folder (the one I told you to rename in a way you knew you'd be copying from it) and paste it into the res folder of your SystemUI project. Choose to overwrite any conflicts.

Note: If you have your own custom images, you would be copying those over instead. However, he_stheone64's XML files still need to be copied if you want all 1% battery steps.

Step 16: Choose option 11 to compile your new SystemUI.apk. Say yes "y" to both prompts.

Note: Having said yes to both prompts you will now have a folder in the root of your APK Manager folder called keep. And you will be prompted to do something with these files. Thus...

Step 17: Delete the resources.arsc file in the root of keep.

Step 18: Delete the drawable and the drawable-xhdpi folders.

Step 19: Back in the script window press any key to finish the compile.

Note: You now have a new file in your place-apk-here-for-modding folder called "unsignedSystemUI.apk". Or rather, "unsignedwhateveryounamedit.apk.

Step 20: Copy the new "unsigned" apk you just compiled and paste into he_stheone64's zipalign folder that I had you create earlier. Run the batchalign.bat file.

Step 21-Zip: If you prefer to use an update zip you can skip these last steps and instead create your zip. Rename the "unsigned" file back into it's proper name, IE: SystemUI.apk, and put it into he_stheone64's update zip, overwriting the one he has in there. That zip is located here: http://www.multiupload.com/Y40E9JNSXH

Step 21-ADB: If you want to use the still-open APK Manager script window to push the SystemUI.apk back on your phone with ADB, then copy and paste your freshly zipaligned file (that you left named "unsigned") BACK into the place-apk-here-for-modding folder.

Step 22-ADB: Choose option 8 and enter the full path of where you want your file to go. In this case "\system\app\SystemUI.apk". The script will automatically rename the file properly and push it to your phone.

Final Step: Reboot.

Congratulations, you now just completed your first UI mod. Hopefully I made the journey a positive experience for you.

Now, I promised to explain a couple of things, so here goes.

Why install into Windows? Well, ADB is a command shell and ideally you would actually be doing all your mod work in the C:\Program Files\Android\android-sdk\platform-tools folder. However, this folder path has a space right between "program" and "files", thus breaking the script tool. The ADB shell is recursive, though, and placing it into Windows allows access to it even if you're not in the proper folder.

Why is the 1.apk file such a big deal (and is the reason I told you to delete everything prior to starting)? This tool is great in that it's built to uncompile and recompile apks across all Android devices. However, when dealing with custom UI's such as TouchWiz or Sense you have a custom framework. For standard every day apks this means nothing. However, for system- or UI-based apks, the framework tells it how to be built to work with the system. It just so happens that ICS is so advanced (or modified, if you prefer) in its UI, and UI-specific apks require the framework to function, we require ICS's framework. This tool isn't updated to recognize a framework-res.apk files as a needed resource since it expects TouchWiz or Sense frameworks, but if you decomplile ICS's framework first, before your failure with decompiling the SystemUI.apk, the tool will extract the framework elements it needs and install them as that 1.apk file. Keep in mind, however, that the tool will create a 1.apk (and other numbers) for ANY decompile that happens first. So if you tried and failed to get that SystemUI.apk to decompile you will already have some files in the apktool folder. And, if you struggled like I have, you'll have a few files in there to clean out.

If you like what I did, please thank this post.