This is my mms.apk and my twframework-res.apk, they are ICS 4.0.3 apks
Ok, I only loaded your twframework with option 81 since it is the only framework you sent us. It decompiled fine. It appeared to recompile fine also except for this:
[*] G:\Sync\Android\AutoAPKTool2.0.4\_INPUT_APK\Mms
recompiling G:\Sync\Android\AutoAPKTool2.0.4\_INPUT_APK\Mms...
I: Copying classes.dex file...
I: Building resources...
aapt: warning: string 'cc_address_label' has no default translation in G:\Sync\Android\AutoAPKTool2.0.4\_INPUT_APK\Mms\res; found: de fr it ko
I: Building apk file...
I don't know what the cc_address_label is but anyway it compiled fine for me otherwise.
Then I used Apk Manager 5.02 with pretty much the exact same results, the log reflects the same string problem but still compiles fine.
Edit: I don't use the AutoAPKtool for everything so I don't know if it tells you or not but some apk files work with the twframework file but not the framework-res file so maybe that is the only problem. Don't use the framework-res (option 1), just the other (option 81) and try it again.
With APK Manager if I use the wrong framework, APK Manager will tell me if it is the wrong dependency so then I have to try the other framework file (in this case twframework).