For those of you who aren't familiar with creating update.zips to deploy your themes or to apply your framework-res.apk changes, I have good news. I've created a program that does it all for you. If you have your folder structure already correct (i.e /system and/or /data exist in the root of the folder), the script can take it from there. It'll even generate the META-INF folder tree structure and the update-script for you if you don't already have one. After creation of the zip, the program will sign it and then you're ready to go. Just copy the zip to your SD card and flash.
Downloads - android-customization-autotool - An all in one Android customization tool that combines existing tools into one application in an easy to use interface - Google Project Hosting
For those of you wondering about the file size, the .exe is relatively large (~6MB) because Py2Exe packages the entire Python interpreter into the .exe. If you have Python installed, you can just download the script from source and save yourself about 6MB in disk space (if it's worth it to you).
If you have any problems, please let me know at:
Issues - android-customization-autotool - An all in one Android customization tool that combines existing tools into one application in an easy to use interface - Google Project Hosting
and I'll do my best to fix them ASAP